--- /dev/null
--- /dev/null
--- /dev/null
--- /dev/null
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++ 8.9000000000000004 1.8800000000000001E-002 -1.1176602466349498E-002 4.8624020454989383E-002 -0.23969485687639777
++ 8.9199999999999999 1.8593999999999999E-002 -9.5192754764016289E-003 3.4242329042405824E-002 -0.28892776111649604
++ 8.9399999999999995 1.8415000000000001E-002 -8.4962956280452053E-003 1.6906663375416429E-002 -0.10459409865658448
++ 8.9600000000000009 1.8251000000000000E-002 -7.9455420114164215E-003 1.0631017456020938E-002 -0.41769584426022249
++ 8.9800000000000004 1.8093000000000001E-002 -8.0215363262878380E-003 -1.4430733199591879E-002 -9.9622524301335516E-002
++ 9.0000000000000000 1.7926000000000001E-002 -8.7183126834330989E-003 -2.0408084657671882E-002 -0.30881405853432908
++ 9.0199999999999996 1.7741000000000000E-002 -9.9052129399811364E-003 -3.8936928169731232E-002 -4.0121241561073183E-002
++ 9.0399999999999991 1.7527000000000001E-002 -1.1510835556643638E-002 -4.1344202663395571E-002 -0.15570097521908205
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++ 9.0800000000000001 1.6993000000000001E-002 -1.5183385109584831E-002 -4.0910752630577585E-002 0.12900040549009040
++ 9.0999999999999996 1.6674000000000001E-002 -1.6665014728219799E-002 -3.3170728301172327E-002 0.32107323560710177
++ 9.1199999999999992 1.6330000000000001E-002 -1.7606555977538157E-002 -1.3906334164746632E-002 0.33670665208557582
++ 9.1400000000000006 1.5975000000000000E-002 -1.7758761361625314E-002 6.2960649603892790E-003 0.58210015604279097
++ 9.1600000000000001 1.5626999999999999E-002 -1.6808398575958429E-002 4.1222074322955993E-002 0.33489272374776108
++ 9.1799999999999997 1.5310000000000001E-002 -1.4757644334542928E-002 6.1315637747821228E-002 0.70332894896548026
++ 9.1999999999999993 1.5044999999999999E-002 -1.1461024085871591E-002 0.10351537468574915 0.22679148039287686
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++ 9.8200000000000003 -1.0770000000000000E-003 3.1833033885575257E-003 2.1336706419000189E-002 -1.2750937923436922
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++ 9.8599999999999994 -9.9500000000000001E-004 -9.0993976657785742E-004 -0.11566102193253433 -0.31709948692764239
++ 9.8800000000000008 -1.0620000000000000E-003 -5.9169000281927651E-003 -0.13468699114819416 0.65159962789105486
++ 9.9000000000000004 -1.2290000000000001E-003 -1.0522460120651184E-002 -9.5591013474731701E-002 1.8357009753638929
++ 9.9199999999999999 -1.4630000000000001E-003 -1.2143259489203794E-002 1.4551045047099517E-002 3.6305964706541420
++ 9.9399999999999995 -1.6710000000000000E-003 -7.2045019225350400E-003 0.23238683328634338 5.2669131420190007
++ 9.9600000000000009 -1.6800000000000001E-003 8.4112671793429763E-003 0.54840162180750474 9.3017509612695566
++ 9.9800000000000004 -1.2179999999999999E-003 4.1509433205165674E-002 1.1065066794836662 6.2760830129074447
++ 10.000000000000000 1.0500000000000000E-004 0.0000000000000000 1.4830716602581049 0.0000000000000000
++ENTROPHY
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++ 2.0600000000000001 275.24737299999998 -2107.6560530000002 -6430.4603729172959 321522.77614586998
++ 2.0800000000000001 233.09424999999999 -1979.0471365416470 12860.906195834919 -116777.46843762224
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++ 2.1200000000000001 168.01675000000000 -1363.6024601247566 6202.8114458544142 -22766.046980826173
++ 2.1400000000000001 143.04369700000001 -1142.8092586675712 4836.8486270048425 -11562.284681313309
++ 2.1600000000000001 122.02975300000000 -963.21005520495339 4143.1115461260433 -11619.564293916252
++ 2.1800000000000002 104.32984000000000 -811.42907051261102 3445.9376884910675 -9158.3331430244616
++ 2.2000000000000002 89.406367000000003 -684.58156274459759 2896.4376999095994 -7785.1031339850051
++ 2.2200000000000002 76.811030000000002 -578.06617850899545 2429.3315118704986 -6465.7543210353215
++ 2.2400000000000002 66.169713000000002 -488.65182321941785 2041.3862526083790 -5407.6295818966191
++ 2.2599999999999998 57.169969999999999 -413.48552861336009 1716.9284776945888 -4548.4773513281798
++ 2.2799999999999998 49.550643000000001 -350.26656232717033 1444.0198366148977 -3707.8360128183176
++ 2.2999999999999998 43.093257000000001 -296.95517207795638 1221.5496758457984 -3485.4285973983156
++ 2.3199999999999998 37.614890000000003 -252.27569936100235 1012.4239600018993 -1512.8245975888249
++ 2.3399999999999999 32.962243000000001 -213.59413047803295 921.65448414656976 -6538.1480122460762
++ 2.3599999999999999 29.006716999999998 -184.57372872686543 529.36560341180484 14170.541646574000
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++ 2.3999999999999999 22.772407000000001 -164.99495281511577 -2309.6230122368133 91733.532649630419
++ 2.4199999999999999 19.282527000000002 -147.29963412503167 3194.3889467410168 -55093.362024471862
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++ 3.2400000000000002 -0.63786699999999996 -1.4719213149640213 17.860439281501677 -48.968676665072060
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--- /dev/null
--- /dev/null
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--- /dev/null
--- /dev/null
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--- /dev/null
--- /dev/null
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--- /dev/null
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++ .0232410908 -.0266146021 -.0163429099
++
++ 2.252000 2.758289 2.828747 2.573807
++ 2.573807 2.314337 3.329045 3.123838
++ 1.679138 1.245463 2.417517 2.138542
++ 2.902927 2.675567 2.916240 2.690005
++ 2.934561 3.360153 2.904943 2.252400
++ 2.822849 3.512073 2.021838 2.021838
++ 0.000000 0.000000 0.000000
++
++ 3.378400 3.464698 3.152444 3.152444
++ 2.834641 4.077473 3.826132 2.056637
++ 1.525464 2.961017 2.619323 3.555555
++ 3.277081 3.571861 3.294765 3.594301
++ 4.115573 3.558025 2.758779 3.457474
++ 4.301648 2.476383 2.476383 0.000000
++ 0.000000 0.000000
++
++ 3.553200 3.232970 3.232970 2.907049
++ 4.181627 3.923866 2.109172 1.564431
++ 3.036654 2.686231 3.646378 3.360790
++ 3.663100 3.378926 3.686114 4.220702
++ 3.648911 2.829249 3.545792 4.411529
++ 2.539639 2.539639 0.000000 0.000000
++ 0.000000
++
++ 2.941600 2.941600 2.645052 3.804760
++ 3.570230 1.919084 1.423437 2.762977
++ 2.444136 3.317750 3.057901 3.332965
++ 3.074402 3.353905 3.840313 3.320055
++ 2.574264 3.226230 4.013942 2.310756
++ 2.310756 0.000000 0.000000 0.000000
++
++
++ 2.941600 2.645052 3.804760 3.570230
++ 1.919084 1.423437 2.762977 2.444136
++ 3.317750 3.057901 3.332965 3.074402
++ 3.353905 3.840313 3.320055 2.574264
++ 3.226230 4.013942 2.310756 2.310756
++ 0.000000 0.000000 0.000000
++
++ 2.378400 3.421196 3.210309 1.725618
++ 1.279938 2.484436 2.197739 2.983282
++ 2.749629 2.996964 2.764467 3.015792
++ 3.453165 2.985354 2.314748 2.900988
++ 3.609290 2.077805 2.077805 0.000000
++ 0.000000 0.000000
++
++ 4.921200 4.617850 2.482205 1.841120
++ 3.573723 3.161325 4.291286 3.955188
++ 4.310965 3.976531 4.338049 4.967185
++ 4.294266 3.329637 4.172909 5.191762
++ 2.988806 2.988806 0.000000 0.000000
++ 0.000000
++
++ 4.333200 2.329199 1.727631 3.353434
++ 2.966456 4.026765 3.711385 4.045231
++ 3.731412 4.070646 4.661001 4.029562
++ 3.124393 3.915686 4.871735 2.804572
++ 2.804572 0.000000 0.000000 0.000000
++
++ 1.252000 0.9286429 1.802551 1.594541
++ 2.164482 1.994958 2.174409 2.005723
++ 2.188069 2.505400 2.165986 1.679436
++ 2.104775 2.618674 1.507524 1.507524
++ 0.000000 0.000000 0.000000
++
++ 0.6888000 1.337002 1.182715 1.605456
++ 1.479715 1.612819 1.487700 1.622951
++ 1.858324 1.606571 1.245684 1.561169
++ 1.942343 1.118173 1.118173 0.000000
++ 0.000000 0.000000
++
++ 2.595200 2.295720 3.116286 2.872216
++ 3.130577 2.887715 3.150245 3.607117
++ 3.118450 2.417947 3.030323 3.770203
++ 2.170439 2.170439 0.000000 0.000000
++ 0.000000
++
++ 2.030800 2.756675 2.540769 2.769316
++ 2.554480 2.786715 3.190865 2.758589
++ 2.138922 2.680631 3.335131 1.919976
++ 1.919976 0.000000 0.000000 0.000000
++
++ 3.742000 3.448923 3.759161 3.467535
++ 3.782778 4.331384 3.744599 2.903442
++ 3.638776 4.527216 2.606238 2.606238
++ 0.000000 0.000000 0.000000
++
++ 3.178800 3.464740 3.195954 3.486507
++ 3.992146 3.451319 2.676042 3.353784
++ 4.172640 2.402115 2.402115 0.000000
++ 0.000000 0.000000
++
++ -7.2938 -4.0239 3.800125 5.9101
++ 3.8743 2.916757 3.655463 4.547977
++ 2.618191 2.618191 0.000000 0.000000
++ 0.000000
++
++ -3.0057 3.505321 6.0636 3.5303
++ 2.690483 3.371882 4.195157 2.415078
++ 2.415078 0.000000 0.000000 0.000000
++
++ 3.824000 4.378585 3.785405 2.935082
++ 3.678429 4.576550 2.634640 2.634640
++ 0.000000 0.000000 0.000000
++
++ -0.1779 -3.4493 3.360749 4.211903
++ 5.240276 3.016734 3.016734 0.000000
++ 0.000000 0.000000
++
++ -9.4378 2.905459 3.641304 4.530360
++ 2.608049 2.608049 0.000000 0.000000
++ 0.000000
++
++ 2.252800 2.823350 3.512697 2.022197
++ 2.022197 0.000000 0.000000 0.000000
++
++
++ 3.538400 4.402332 2.534345 2.534345
++ 0.000000 0.000000 0.000000
++
++ 5.477200 3.153127 3.153127 0.000000
++ 0.000000 0.000000
++
++ 1.815200 1.815200 0.000000 0.000000
++ 0.000000
++
++ 1.815200 0.000000 0.000000 0.000000
++
++ 0.000000 0.000000 0.000000
++
++ 0.000000 0.000000
++
++ 0.000000
++
--- /dev/null
--- /dev/null
++ 6 6 0
++0 0 0 0 0 0 0 0 0 0 2 2 2 2 -1 -1 2 1 1 0
++0.000210 6.89 0.100 0.100 -0.188 -0.188 0.50 3.24 3.88 32.100 5.330 5.33 0.08 0.08 1 0.00 0.00 0.00 0.00 0.60 0.00 0.60 0.00 0.00 0.00 0.0000 0.00 0.00 0.00 2.82 184.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00 Cys Cys
++0.001570 5.70 0.003 0.286 -0.998 0.207 0.50 3.56 3.72 4.400 4.030 7.57 -0.04 0.04 1 0.00 0.00 0.00 0.00 0.60 0.00 1.50 0.00 0.00 0.00 0.0000 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00 Met Cys
++0.055600 4.39 0.587 0.587 0.892 0.892 9.13 -0.27 0.66 33.100 9.590 9.59 0.21 0.21 1 0.00 0.00 0.00 0.00 2.50 0.00 2.50 0.00 0.00 0.00 0.0000 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00 Met Met
++0.000020 7.55 -0.011 0.167 -0.998 -0.036 0.00 0.05 2.26 4.700 3.550 6.67 0.03 0.20 1 0.00 0.00 0.00 0.00 0.60 0.00 1.50 0.00 0.00 0.00 0.0000 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00 Phe Cys
++0.000800 6.01 0.374 0.370 -0.487 0.078 0.60 4.39 4.00 4.500 7.780 3.78 0.28 0.17 1 0.00 0.00 0.00 0.00 2.50 0.00 2.50 0.00 0.00 0.00 0.0000 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00 Phe Met
++0.058900 4.76 0.581 0.581 0.914 0.914 0.84 2.88 2.84 33.100 10.800 10.80 0.16 0.16 1 0.00 0.00 0.00 0.00 2.50 0.00 2.50 0.00 0.00 0.00 0.0000 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00 Phe Phe
++0.000290 7.36 -0.030 0.186 -0.998 0.225 0.80 4.59 4.41 4.400 3.730 7.02 0.04 0.08 1 0.00 0.00 0.00 0.00 0.60 0.00 1.50 0.00 0.00 0.00 0.0000 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00 Ile Cys
++0.010800 5.45 0.444 0.464 0.419 0.960 42.40 -0.07 0.22 32.700 6.900 7.04 0.27 0.21 1 0.00 0.00 0.00 0.00 2.50 0.00 2.50 0.00 0.00 0.00 0.0000 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00 Ile Met
++0.000600 6.79 0.346 0.279 -0.372 0.371 0.80 4.44 3.96 4.500 8.000 3.89 0.25 0.13 1 0.00 0.00 0.00 0.00 2.50 0.00 2.50 0.00 0.00 0.00 0.0000 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00 Ile Phe
++0.010700 6.20 0.322 0.322 0.546 0.546 135.50 -0.59 0.42 14.400 10.400 10.40 0.17 0.17 1 0.00 0.00 0.00 0.00 2.50 0.00 2.50 0.00 0.00 0.00 0.0000 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00 Ile Ile
++0.000290 7.36 -0.030 0.186 -0.998 0.225 0.80 4.59 4.41 4.400 3.730 7.02 0.04 0.08 1 0.00 0.00 0.00 0.00 0.60 0.00 1.50 0.00 0.00 0.00 0.0000 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00 Leu Cys
++0.010800 5.45 0.444 0.464 0.419 0.960 42.40 -0.07 0.22 32.700 6.900 7.04 0.27 0.21 1 0.00 0.00 0.00 0.00 2.50 0.00 2.50 0.00 0.00 0.00 0.0000 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00 Leu Met
++0.000600 6.79 0.346 0.279 -0.372 0.371 0.80 4.44 3.96 4.500 8.000 3.89 0.25 0.13 1 0.00 0.00 0.00 0.00 2.50 0.00 2.50 0.00 0.00 0.00 0.0000 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00 Leu Phe
++0.010700 6.20 0.322 0.000 0.546 0.000 135.50 -0.59 0.42 14.400 10.400 0.00 0.17 0.00 1 0.00 0.00 0.00 0.00 2.50 0.00 2.50 0.00 0.00 0.00 0.0000 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00 Leu Ile
++0.010700 6.20 0.322 0.322 0.546 0.546 135.50 -0.59 0.42 14.400 10.400 10.40 0.17 0.17 1 0.00 0.00 0.00 0.00 2.50 0.00 2.50 0.00 0.00 0.00 0.0000 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00 Leu Leu
++0.002470 6.21 0.001 0.009 -0.998 0.078 1.00 4.58 4.23 4.400 3.600 6.76 0.07 0.05 1 0.00 0.00 0.00 0.00 0.60 0.00 1.50 0.00 0.00 0.00 0.0000 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00 Val Cys
++0.016800 5.21 0.586 0.253 0.969 0.531 12.80 0.50 0.75 11.000 4.630 6.42 0.06 -0.07 1 0.00 0.00 0.00 0.00 2.50 0.00 2.50 0.00 0.00 0.00 0.0000 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00 Val Met
++0.001800 6.02 0.308 0.414 0.734 0.314 1.00 2.77 2.49 3.800 4.280 8.04 0.04 0.20 1 0.00 0.00 0.00 0.00 2.50 0.00 2.50 0.00 0.00 0.00 0.0000 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00 Val Phe
++0.023600 5.69 0.425 0.245 0.990 0.250 30.10 0.05 0.30 31.900 5.690 7.89 0.07 -0.20 1 0.00 0.00 0.00 0.00 2.50 0.00 2.50 0.00 0.00 0.00 0.0000 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00 Val Ile
++0.023600 5.69 0.425 0.245 0.990 0.250 30.10 0.05 0.30 31.900 5.690 7.89 0.07 -0.20 1 0.00 0.00 0.00 0.00 2.50 0.00 2.50 0.00 0.00 0.00 0.0000 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00 Val Leu
++0.002300 7.05 0.158 0.158 0.267 0.267 149.80 -0.56 0.45 5.840 8.890 8.89 0.10 0.10 1 0.00 0.00 0.00 0.00 2.50 0.00 2.50 0.00 0.00 0.00 0.0000 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00 Val Val
++0.000030 7.11 0.112 0.089 -0.998 -0.032 0.20 3.69 3.44 4.100 4.830 9.08 -0.10 -0.13 1 0.00 0.00 0.00 0.00 1.50 0.00 0.60 0.00 0.00 0.00 0.0000 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00 Trp Cys
++0.001800 5.46 0.481 0.411 -0.505 0.191 0.60 4.24 4.12 4.500 8.160 3.97 0.22 0.15 1 0.00 0.00 0.00 0.00 2.50 0.00 2.50 0.00 0.00 0.00 0.0000 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00 Trp Met
++0.046000 4.64 0.591 0.681 0.896 0.998 0.60 3.04 5.19 4.100 10.340 5.03 0.06 0.53 1 0.00 0.00 0.00 0.00 2.50 0.00 2.50 0.00 0.00 0.00 0.0000 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00 Trp Phe
++0.006200 5.33 0.547 0.445 0.428 0.978 0.60 4.37 4.03 4.500 8.230 4.00 0.23 0.02 1 0.00 0.00 0.00 0.00 2.50 0.00 2.50 0.00 0.00 0.00 0.0000 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00 Trp Ile
++0.006200 5.33 0.547 0.445 0.428 0.978 0.60 4.37 4.03 4.500 8.230 4.00 0.23 0.02 1 0.00 0.00 0.00 0.00 2.50 0.00 2.50 0.00 0.00 0.00 0.0000 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00 Trp Leu
++0.002400 5.72 0.505 0.310 0.424 0.779 0.60 4.35 4.05 4.500 8.230 4.00 0.19 -0.07 1 0.00 0.00 0.00 0.00 2.50 0.00 2.50 0.00 0.00 0.00 0.0000 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00 Trp Val
++0.189100 3.86 0.750 0.750 0.992 0.992 6.82 -1.03 0.35 32.700 8.720 8.72 0.00 0.00 1 0.00 0.00 0.00 0.00 2.50 0.00 2.50 0.00 0.00 0.00 0.0000 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00 Trp Trp
++0.000730 5.61 0.101 0.148 -0.997 0.120 0.00 4.23 4.34 4.200 4.310 8.11 -0.10 -0.07 1 0.00 0.00 0.00 0.00 0.60 0.00 0.60 0.00 0.00 0.00 0.0000 0.00 0.00 0.00 1.70 179.36 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00 Tyr Cys
++0.000040 7.13 0.062 0.203 -0.998 0.074 0.60 3.84 3.31 3.900 5.220 9.81 -0.20 -0.07 1 0.00 0.00 0.00 0.00 0.60 0.00 1.50 0.00 0.00 0.00 0.0000 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00 Tyr Met
++0.000030 8.16 0.015 0.129 -0.998 0.056 0.50 4.59 4.11 3.800 5.230 9.83 -0.01 -0.36 1 0.00 0.00 0.00 0.00 1.50 0.00 0.60 0.00 0.00 0.00 0.0000 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00 Tyr Phe
++0.000100 7.30 0.084 0.196 -0.998 0.199 0.60 4.52 4.24 4.100 4.580 8.61 -0.08 -0.06 1 0.00 0.00 0.00 0.00 0.60 0.00 1.50 0.00 0.00 0.00 0.0000 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00 Tyr Ile
++0.000100 7.30 0.084 0.196 -0.998 0.199 0.60 4.52 4.24 4.100 4.580 8.61 -0.08 -0.06 1 0.00 0.00 0.00 0.00 0.60 0.00 1.50 0.00 0.00 0.00 0.0000 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00 Tyr Leu
++0.000050 7.85 0.083 0.081 -0.998 0.059 0.40 4.44 4.39 4.200 4.370 8.21 -0.04 -0.01 1 0.00 0.00 0.00 0.00 0.60 0.00 1.50 0.00 0.00 0.00 0.0000 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00 Tyr Val
++0.000010 8.49 0.027 0.091 -0.998 -0.024 0.50 4.67 3.93 3.400 5.820 10.95 -0.03 -0.33 1 0.00 0.00 0.00 0.00 1.50 0.00 0.60 0.00 0.00 0.00 0.0000 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00 Tyr Trp
++0.000180 6.88 0.065 0.065 -0.317 -0.317 0.70 4.10 3.37 32.100 8.530 8.53 -0.23 -0.23 1 0.00 0.00 0.00 0.00 0.60 0.00 0.60 0.00 0.00 0.00 0.0000 0.00 0.00 0.00 0.08 183.49 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00 Tyr Tyr
++0.002090 5.63 0.013 0.186 -0.998 0.118 0.90 4.51 4.22 4.600 3.240 6.08 0.09 0.07 1 0.00 0.00 0.00 0.00 0.60 0.00 1.50 0.00 0.00 0.00 0.0000 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00 Ala Cys
++0.007400 5.00 0.377 0.383 0.821 0.386 37.00 -0.01 0.20 31.300 5.380 7.46 0.10 0.83 1 0.00 0.00 0.00 0.00 2.50 0.00 2.50 0.00 0.00 0.00 0.0000 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00 Ala Met
++0.000100 7.17 0.142 0.206 -0.006 -0.750 0.50 4.39 3.96 4.300 3.900 7.33 0.07 0.09 1 0.00 0.00 0.00 0.00 2.50 0.00 2.50 0.00 0.00 0.00 0.0000 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00 Ala Phe
++0.000400 7.20 0.154 0.249 0.088 0.704 37.00 -0.00 0.25 31.300 5.340 7.41 0.10 0.13 1 0.00 0.00 0.00 0.00 2.50 0.00 2.50 0.00 0.00 0.00 0.0000 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00 Ala Ile
++0.000400 7.20 0.154 0.249 0.088 0.704 37.00 -0.00 0.25 31.300 5.340 7.41 0.10 0.13 1 0.00 0.00 0.00 0.00 2.50 0.00 2.50 0.00 0.00 0.00 0.0000 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00 Ala Leu
++0.000500 7.01 0.111 0.317 0.121 0.869 27.60 0.08 0.34 32.100 5.080 7.05 0.08 0.07 1 0.00 0.00 0.00 0.00 2.50 0.00 2.50 0.00 0.00 0.00 0.0000 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00 Ala Val
++0.000100 7.03 0.324 0.103 -0.290 -0.096 0.50 4.41 3.94 4.500 8.010 3.90 0.08 -0.12 1 0.00 0.00 0.00 0.00 2.50 0.00 2.50 0.00 0.00 0.00 0.0000 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00 Ala Trp
++0.000040 7.12 0.099 0.100 -0.998 0.023 0.30 4.37 4.23 4.200 4.260 8.01 -0.10 -0.10 1 0.00 0.00 0.00 0.00 0.60 0.00 1.50 0.00 0.00 0.00 0.0000 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00 Ala Tyr
++0.000500 6.40 0.238 0.238 0.503 0.503 16.60 -0.08 0.78 31.700 7.460 7.46 0.16 0.16 1 0.00 0.00 0.00 0.00 2.50 0.00 2.50 0.00 0.00 0.00 0.0000 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00 Ala Ala
++0.004010 5.08 0.097 0.005 -0.588 0.024 0.80 4.56 4.22 4.600 3.100 5.83 0.10 -0.00 1 0.00 0.00 0.00 0.00 0.60 0.00 1.50 0.00 0.00 0.00 0.0000 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00 Gly Cys
++0.000002 9.49 0.124 -0.006 -0.997 -0.085 36.10 -0.12 0.20 31.300 5.160 7.16 0.23 -0.12 1 0.00 0.00 0.00 0.00 2.50 0.00 2.50 0.00 0.00 0.00 0.0000 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00 Gly Met
++0.000010 6.93 0.423 0.033 -0.997 0.225 36.70 -0.55 -0.02 31.400 3.330 4.62 0.53 -0.04 1 0.00 0.00 0.00 0.00 2.50 0.00 2.50 0.00 0.00 0.00 0.0000 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00 Gly Phe
++0.000020 8.79 0.018 -0.011 -0.997 -0.042 36.70 -0.05 0.25 31.300 4.940 6.86 0.15 -0.07 1 0.00 0.00 0.00 0.00 2.50 0.00 2.50 0.00 0.00 0.00 0.0000 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00 Gly Ile
++0.000020 8.79 0.018 -0.011 -0.997 -0.042 36.70 -0.05 0.25 31.300 4.940 6.86 0.15 -0.07 1 0.00 0.00 0.00 0.00 2.50 0.00 2.50 0.00 0.00 0.00 0.0000 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00 Gly Leu
++0.000100 7.69 -0.036 0.007 -0.997 0.000 36.90 -0.03 0.27 31.300 4.800 6.66 0.11 -0.02 1 0.00 0.00 0.00 0.00 2.50 0.00 2.50 0.00 0.00 0.00 0.0000 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00 Gly Val
++0.000002 8.05 0.132 0.004 -0.997 0.014 36.20 -0.47 0.04 31.400 3.140 4.36 0.62 -0.04 1 0.00 0.00 0.00 0.00 2.50 0.00 2.50 0.00 0.00 0.00 0.0000 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00 Gly Trp
++0.000350 5.53 0.143 -0.013 -0.998 -0.062 0.00 3.83 3.76 4.400 3.990 7.51 -0.07 0.00 1 0.00 0.00 0.00 0.00 0.60 0.00 1.50 0.00 0.00 0.00 0.0000 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00 Gly Tyr
++0.000020 7.92 0.039 0.005 -0.997 0.002 36.80 -0.02 0.30 31.300 4.240 5.88 0.19 0.01 1 0.00 0.00 0.00 0.00 2.50 0.00 2.50 0.00 0.00 0.00 0.0000 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00 Gly Ala
++0.004000 5.13 0.000 0.000 0.000 0.000 90.00 -39.90 50.60 0.010 0.000 0.00 0.00 0.00 1 0.00 0.00 0.00 0.00 2.50 0.00 2.50 0.00 0.00 0.00 0.0000 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00 Gly Gly
++0.003360 5.83 -0.032 0.161 -0.997 0.084 0.70 4.47 4.32 4.500 3.360 6.31 0.13 0.07 1 0.00 0.00 0.00 0.00 0.60 0.00 0.60 0.00 0.00 0.00 0.0000 0.00 0.00 0.00 0.60 179.41 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00 Thr Cys
++0.001400 6.08 -0.032 0.240 -0.998 0.063 0.60 3.60 3.68 4.400 3.930 7.38 0.09 0.08 1 0.00 0.00 0.00 0.00 0.60 0.00 1.50 0.00 0.00 0.00 0.0000 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00 Thr Met
++0.000020 8.08 -0.019 0.146 -0.998 -0.056 0.00 0.04 2.19 4.700 3.430 6.45 0.16 0.21 1 0.00 0.00 0.00 0.00 0.60 0.00 1.50 0.00 0.00 0.00 0.0000 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00 Thr Phe
++0.004530 6.10 -0.008 0.232 -0.998 0.259 1.00 3.70 3.66 4.500 3.720 7.00 0.11 0.10 1 0.00 0.00 0.00 0.00 0.60 0.00 1.50 0.00 0.00 0.00 0.0000 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00 Thr Ile
++0.004530 6.10 -0.008 0.232 -0.998 0.259 1.00 3.70 3.66 4.500 3.720 7.00 0.11 0.10 1 0.00 0.00 0.00 0.00 0.60 0.00 1.50 0.00 0.00 0.00 0.0000 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00 Thr Leu
++0.005070 6.13 0.043 0.078 -0.553 0.012 1.00 4.60 4.21 4.400 3.620 6.80 0.12 0.05 1 0.00 0.00 0.00 0.00 0.60 0.00 1.50 0.00 0.00 0.00 0.0000 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00 Thr Val
++0.000006 8.23 0.128 0.115 -0.998 0.073 0.00 0.01 2.47 4.700 3.610 6.78 0.30 0.09 1 0.00 0.00 0.00 0.00 1.50 0.00 0.60 0.00 0.00 0.00 0.0000 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00 Thr Trp
++0.000030 7.52 -0.005 0.202 -0.997 0.067 0.00 2.49 3.75 4.500 3.740 7.03 0.06 0.08 1 0.00 0.00 0.00 0.00 0.60 0.00 0.60 0.00 0.00 0.00 0.0000 0.00 0.00 0.00 1.49 179.40 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00 Thr Tyr
++0.003690 5.57 0.042 0.176 -0.732 0.079 0.90 4.53 4.28 4.500 3.250 6.10 0.15 0.07 1 0.00 0.00 0.00 0.00 0.60 0.00 1.50 0.00 0.00 0.00 0.0000 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00 Thr Ala
++0.003770 5.40 0.045 -0.036 -0.669 -0.071 0.90 4.59 4.22 4.600 3.100 5.83 0.17 -0.01 1 0.00 0.00 0.00 0.00 0.60 0.00 1.50 0.00 0.00 0.00 0.0000 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00 Thr Gly
++0.000050 8.64 0.043 0.043 -0.252 -0.252 1.10 4.04 3.25 32.100 6.090 6.09 0.14 0.14 1 0.00 0.00 0.00 0.00 0.60 0.00 0.60 0.00 0.00 0.00 0.0000 0.00 0.00 0.00 0.05 184.10 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00 Thr Thr
++0.003910 5.43 0.024 0.177 -0.997 0.123 0.70 4.57 4.20 4.500 3.320 6.24 0.10 0.08 1 0.00 0.00 0.00 0.00 0.60 0.00 0.60 0.00 0.00 0.00 0.0000 0.00 0.00 0.00 0.58 179.42 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00 Ser Cys
++0.000120 7.04 -0.008 0.220 -0.998 0.061 0.40 4.49 4.39 4.400 3.770 7.08 0.01 0.08 1 0.00 0.00 0.00 0.00 0.60 0.00 1.50 0.00 0.00 0.00 0.0000 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00 Ser Met
++0.000010 7.91 -0.063 0.109 -0.998 -0.248 0.00 0.01 2.20 4.700 3.430 6.45 0.06 0.27 1 0.00 0.00 0.00 0.00 0.60 0.00 1.50 0.00 0.00 0.00 0.0000 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00 Ser Phe
++0.000500 6.99 0.003 0.199 -0.998 0.262 0.80 4.57 4.41 4.500 3.580 6.73 0.06 0.07 1 0.00 0.00 0.00 0.00 0.60 0.00 1.50 0.00 0.00 0.00 0.0000 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00 Ser Ile
++0.000500 6.99 0.003 0.199 -0.998 0.262 0.80 4.57 4.41 4.500 3.580 6.73 0.06 0.07 1 0.00 0.00 0.00 0.00 0.60 0.00 1.50 0.00 0.00 0.00 0.0000 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00 Ser Leu
++0.006700 5.73 0.092 0.082 -0.410 0.019 0.90 4.55 4.26 4.500 3.460 6.50 0.10 0.06 1 0.00 0.00 0.00 0.00 0.60 0.00 1.50 0.00 0.00 0.00 0.0000 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00 Ser Val
++0.000020 7.11 0.108 0.100 -0.998 -0.041 0.00 0.06 2.15 4.700 3.350 6.29 0.47 0.49 1 0.00 0.00 0.00 0.00 1.50 0.00 0.60 0.00 0.00 0.00 0.0000 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00 Ser Trp
++0.000020 7.60 -0.037 0.179 -0.997 0.221 0.00 2.91 3.62 4.500 3.960 7.44 -0.06 -0.00 1 0.00 0.00 0.00 0.00 0.60 0.00 0.60 0.00 0.00 0.00 0.0000 0.00 0.00 0.00 1.58 179.38 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00 Ser Tyr
++0.004000 5.39 0.093 0.158 -0.554 -0.061 1.10 4.59 4.28 4.600 3.070 5.77 0.14 0.11 1 0.00 0.00 0.00 0.00 0.60 0.00 1.50 0.00 0.00 0.00 0.0000 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00 Ser Ala
++0.006100 4.97 0.109 -0.032 -0.545 -0.079 0.90 4.63 4.19 4.600 2.980 5.60 0.16 -0.01 1 0.00 0.00 0.00 0.00 0.60 0.00 1.50 0.00 0.00 0.00 0.0000 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00 Ser Gly
++0.002550 5.85 -0.001 0.131 -0.997 0.067 0.70 4.53 4.25 4.500 3.340 6.27 0.10 0.14 1 0.00 0.00 0.00 0.00 0.60 0.00 0.60 0.00 0.00 0.00 0.0000 0.00 0.00 0.00 0.41 179.42 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00 Ser Thr
++0.000160 6.86 0.076 0.076 -0.315 -0.315 0.50 3.41 3.76 32.100 4.900 4.90 0.13 0.13 1 0.00 0.00 0.00 0.00 0.60 0.00 0.60 0.00 0.00 0.00 0.0000 0.00 0.00 0.00 2.78 184.01 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00 Ser Ser
++0.002540 5.70 -0.012 0.257 -0.997 0.250 0.40 4.37 4.36 4.400 3.640 6.85 0.01 0.03 1 0.00 0.00 0.00 0.00 0.60 0.00 0.60 0.00 0.00 0.00 0.0000 0.00 0.00 0.00 0.41 179.42 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00 Gln Cys
++0.000100 7.40 0.044 0.201 -0.998 0.217 0.60 3.72 3.54 4.200 4.420 8.31 -0.00 -0.05 1 0.00 0.00 0.00 0.00 0.60 0.00 1.50 0.00 0.00 0.00 0.0000 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00 Gln Met
++0.000020 7.68 0.086 0.148 -0.998 -0.042 0.00 2.66 3.95 4.400 4.090 7.70 0.02 0.09 1 0.00 0.00 0.00 0.00 0.60 0.00 1.50 0.00 0.00 0.00 0.0000 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00 Gln Phe
++0.001830 6.36 0.105 0.218 -0.998 0.336 0.90 3.77 3.63 4.400 4.010 7.53 0.07 0.04 1 0.00 0.00 0.00 0.00 0.60 0.00 1.50 0.00 0.00 0.00 0.0000 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00 Gln Ile
++0.001830 6.36 0.105 0.218 -0.998 0.336 0.90 3.77 3.63 4.400 4.010 7.53 0.07 0.04 1 0.00 0.00 0.00 0.00 0.60 0.00 1.50 0.00 0.00 0.00 0.0000 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00 Gln Leu
++0.000200 7.69 0.069 0.081 -0.998 0.109 1.00 3.79 3.63 4.500 3.750 7.05 0.09 0.04 1 0.00 0.00 0.00 0.00 0.60 0.00 1.50 0.00 0.00 0.00 0.0000 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00 Gln Val
++0.000070 6.72 0.109 0.255 -0.998 0.289 0.50 3.83 3.28 3.800 5.270 9.90 -0.12 -0.10 1 0.00 0.00 0.00 0.00 1.50 0.00 0.60 0.00 0.00 0.00 0.0000 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00 Gln Trp
++0.000820 5.66 0.072 0.259 -0.997 0.120 0.20 4.00 4.69 4.300 4.150 7.80 -0.03 -0.02 1 0.00 0.00 0.00 0.00 0.60 0.00 0.60 0.00 0.00 0.00 0.0000 0.00 0.00 0.00 0.34 179.43 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00 Gln Tyr
++0.000900 6.01 0.074 0.154 -0.998 0.109 0.60 4.51 4.18 4.430 3.640 6.85 0.06 -0.01 1 0.00 0.00 0.00 0.00 0.60 0.00 1.50 0.00 0.00 0.00 0.0000 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00 Gln Ala
++0.000840 5.79 0.113 -0.112 -0.755 -0.409 0.50 4.57 4.15 4.500 3.460 6.50 0.15 0.00 1 0.00 0.00 0.00 0.00 0.60 0.00 1.50 0.00 0.00 0.00 0.0000 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00 Gln Gly
++0.003950 5.74 -0.027 0.279 -0.997 0.267 0.50 4.43 4.31 4.400 3.610 6.79 0.12 0.12 1 0.00 0.00 0.00 0.00 0.60 0.00 0.60 0.00 0.00 0.00 0.0000 0.00 0.00 0.00 0.47 179.42 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00 Gln Thr
++0.002440 5.71 -0.015 0.231 -0.997 0.184 0.50 4.42 4.31 4.500 3.560 6.70 0.05 0.05 1 0.00 0.00 0.00 0.00 0.60 0.00 0.60 0.00 0.00 0.00 0.0000 0.00 0.00 0.00 0.34 179.42 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00 Gln Ser
++0.000170 7.27 0.118 0.118 -0.228 -0.228 0.60 3.98 3.57 32.100 6.730 6.73 0.06 0.06 1 0.00 0.00 0.00 0.00 0.60 0.00 0.60 0.00 0.00 0.00 0.0000 0.00 0.00 0.00 0.02 183.34 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00 Gln Gln
++0.001540 5.80 -0.009 0.163 -0.997 -0.039 0.50 4.44 4.29 4.500 3.520 6.62 0.06 0.09 1 0.00 0.00 0.00 0.00 0.60 0.00 0.60 0.00 0.00 0.00 0.0000 0.00 0.00 0.00 0.41 179.42 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00 Asn Cys
++0.001930 5.61 0.043 0.296 -0.998 0.285 0.50 3.60 3.67 4.400 4.070 7.66 0.00 0.00 1 0.00 0.00 0.00 0.00 0.60 0.00 1.50 0.00 0.00 0.00 0.0000 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00 Asn Met
++0.000030 7.43 0.014 0.158 -0.998 -0.051 0.00 0.10 2.30 4.700 3.510 6.60 0.06 0.20 1 0.00 0.00 0.00 0.00 0.60 0.00 1.50 0.00 0.00 0.00 0.0000 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00 Asn Phe
++0.002810 6.00 0.041 0.216 -0.998 0.217 0.70 4.40 4.46 4.400 3.660 6.87 0.09 0.06 1 0.00 0.00 0.00 0.00 0.60 0.00 1.50 0.00 0.00 0.00 0.0000 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00 Asn Ile
++0.002810 6.00 0.041 0.216 -0.998 0.217 0.70 4.40 4.46 4.400 3.660 6.87 0.09 0.06 1 0.00 0.00 0.00 0.00 0.60 0.00 1.50 0.00 0.00 0.00 0.0000 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00 Asn Leu
++0.001690 6.27 0.037 0.089 -0.998 0.058 0.80 4.61 4.22 4.400 3.720 6.98 0.12 0.04 1 0.00 0.00 0.00 0.00 0.60 0.00 1.50 0.00 0.00 0.00 0.0000 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00 Asn Val
++0.000040 7.18 0.082 0.117 -0.998 0.035 0.40 3.78 3.36 3.900 5.240 9.85 -0.20 -0.05 1 0.00 0.00 0.00 0.00 1.50 0.00 0.60 0.00 0.00 0.00 0.0000 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00 Asn Trp
++0.000040 7.30 0.064 0.130 -0.997 0.065 0.20 4.44 4.46 4.200 4.380 8.23 -0.05 -0.01 1 0.00 0.00 0.00 0.00 0.60 0.00 0.60 0.00 0.00 0.00 0.0000 0.00 0.00 0.00 0.11 179.48 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00 Asn Tyr
++0.002360 5.43 0.123 0.148 -0.495 -0.052 0.60 4.46 4.30 4.500 3.360 6.31 0.13 0.02 1 0.00 0.00 0.00 0.00 0.60 0.00 1.50 0.00 0.00 0.00 0.0000 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00 Asn Ala
++0.002350 5.17 0.120 -0.062 -0.474 -0.218 0.50 4.65 4.05 4.500 3.370 6.33 0.16 -0.01 1 0.00 0.00 0.00 0.00 0.60 0.00 1.50 0.00 0.00 0.00 0.0000 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00 Asn Gly
++0.002840 5.75 -0.019 0.195 -0.997 0.081 0.50 4.40 4.35 4.500 3.470 6.52 0.13 0.12 1 0.00 0.00 0.00 0.00 0.60 0.00 0.60 0.00 0.00 0.00 0.0000 0.00 0.00 0.00 0.40 179.42 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00 Asn Thr
++0.001910 5.65 0.006 0.184 -0.997 0.031 0.50 4.50 4.24 4.500 3.430 6.44 0.08 0.13 1 0.00 0.00 0.00 0.00 0.60 0.00 0.60 0.00 0.00 0.00 0.0000 0.00 0.00 0.00 0.33 179.42 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00 Asn Ser
++0.000090 7.48 0.008 0.176 -0.997 0.079 0.20 3.85 4.83 4.500 3.450 6.49 0.11 0.08 1 0.00 0.00 0.00 0.00 0.60 0.00 0.60 0.00 0.00 0.00 0.0000 0.00 0.00 0.00 0.01 179.44 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00 Asn Gln
++0.000060 7.65 0.079 0.079 -0.269 -0.269 0.03 3.16 4.26 32.100 5.650 5.65 0.10 0.10 1 0.00 0.00 0.00 0.00 0.60 0.00 0.60 0.00 0.00 0.00 0.0000 0.00 0.00 0.00 0.00 183.35 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00 Asn Asn
++0.000090 7.82 0.033 0.126 -0.998 0.130 1.00 4.60 4.21 4.500 3.460 6.51 0.01 0.04 1 0.00 0.00 0.00 0.00 0.50 0.00 0.60 0.00 0.60 0.00 0.0100 2.86 1.14 2.08 0.00 1.15 0.00 0.69 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00 Glu Cys
++0.001590 6.00 -0.311 0.205 -0.998 0.011 7.60 3.86 0.64 13.500 4.410 7.95 -0.25 0.15 1 0.00 0.00 0.00 0.00 0.50 0.00 1.50 0.00 0.60 0.00 0.0000 0.00 2.80 3.52 0.00 0.00 0.00 1.26 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00 Glu Met
++0.000800 6.25 -0.422 0.150 -0.998 -0.300 7.30 0.01 0.48 13.600 4.060 7.32 -0.23 0.26 1 0.00 0.00 0.00 0.00 0.50 0.00 1.50 0.00 0.60 0.00 0.0000 0.00 2.07 2.72 0.00 0.00 0.00 1.24 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00 Glu Phe
++0.000470 7.34 -0.150 0.195 -0.998 0.348 7.70 0.55 0.79 13.600 4.190 7.55 0.35 -0.12 1 0.00 0.00 0.00 0.00 0.50 0.00 1.50 0.00 0.60 0.00 0.0000 0.00 2.76 3.49 0.00 0.00 0.00 0.08 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00 Glu Ile
++0.000470 7.34 -0.150 0.195 -0.998 0.348 7.70 0.55 0.79 13.600 4.190 7.55 0.35 -0.12 1 0.00 0.00 0.00 0.00 0.50 0.00 1.50 0.00 0.60 0.00 0.0000 0.00 2.76 3.49 0.00 0.00 0.00 0.08 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00 Glu Leu
++0.000110 8.25 -0.117 0.079 -0.998 0.148 7.60 0.64 0.84 13.600 4.070 7.33 -0.08 0.06 1 0.00 0.00 0.00 0.00 0.50 0.00 1.50 0.00 0.60 0.00 0.0000 0.00 1.86 2.96 0.00 0.00 0.00 1.10 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00 Glu Val
++0.000590 5.95 -0.587 0.202 -0.998 -0.335 4.90 0.01 0.53 13.700 4.130 7.44 -0.29 0.29 1 0.00 0.00 0.00 0.00 0.50 0.00 1.50 0.00 0.60 0.00 0.0000 0.00 1.45 2.63 0.00 0.00 0.00 1.16 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00 Glu Trp
++0.000006 9.65 -0.043 0.135 -0.998 -0.029 0.00 0.00 2.33 4.800 3.400 4.55 -0.07 0.29 1 0.00 0.00 0.00 0.00 0.50 0.00 0.60 0.00 0.60 0.00 0.0100 2.25 1.03 2.02 0.00 1.00 0.00 0.03 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00 Glu Tyr
++0.000240 7.01 -0.149 0.139 -0.998 0.184 7.60 0.52 0.77 13.600 3.790 6.83 -0.13 0.06 1 0.00 0.00 0.00 0.00 0.50 0.00 1.50 0.00 0.60 0.00 0.0000 0.00 1.68 2.70 0.00 0.00 0.00 0.98 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00 Glu Ala
++0.000190 6.83 -0.140 -0.031 -0.998 -0.110 7.60 0.53 0.72 13.600 3.540 6.39 -0.05 0.03 1 0.00 0.00 0.00 0.00 0.50 0.00 1.50 0.00 0.60 0.00 0.0000 0.00 1.60 2.65 0.00 0.00 0.00 0.82 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00 Glu Gly
++0.000210 7.52 0.042 0.098 -0.998 0.129 0.80 4.60 4.19 4.500 3.550 6.67 0.04 0.08 1 0.00 0.00 0.00 0.00 0.50 0.00 0.60 0.00 0.60 0.00 0.0100 2.96 0.93 1.96 0.01 1.12 0.00 0.08 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00 Glu Thr
++0.000270 6.91 0.050 0.098 -0.998 -0.026 0.70 4.67 4.10 4.500 3.410 6.42 0.11 0.16 1 0.00 0.00 0.00 0.00 0.50 0.00 0.60 0.00 0.60 0.00 0.0100 3.37 0.96 1.98 5.29 1.24 0.00 0.09 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00 Glu Ser
++0.000150 7.51 0.035 0.195 -0.998 0.187 0.70 4.62 4.10 4.400 3.820 7.18 -0.01 0.05 1 0.00 0.00 0.00 0.00 0.50 0.00 0.60 0.00 0.60 0.00 0.0100 2.82 1.05 2.03 0.00 1.19 0.00 0.18 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00 Glu Gln
++0.002240 5.76 0.072 0.211 -0.998 0.162 0.70 4.48 4.27 4.500 3.570 6.72 -0.04 0.08 1 0.00 0.00 0.00 0.00 0.50 0.00 0.60 0.00 0.60 0.00 0.0100 2.96 1.04 2.02 0.01 1.16 0.00 0.63 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00 Glu Asn
++0.000002 5.57 -0.996 -0.996 -0.990 -0.990 0.08 -62.40 6.34 13.000 4.530 4.53 0.08 0.08 1 0.00 0.00 0.00 0.00 0.50 0.00 0.50 0.00 0.60 0.60 0.0080 4.89 0.34 0.34 0.00 0.00 0.00 0.84 0.84 13.60 -13.80 0.52 33.30 9.31 9.31 1.00 Glu Glu
++0.002000 5.94 -0.019 0.151 -0.998 0.067 1.00 4.64 4.18 4.500 3.260 6.13 0.10 0.06 1 0.00 0.00 0.00 0.00 0.50 0.00 0.60 0.00 0.50 0.00 0.0100 3.60 2.96 3.97 0.13 0.99 0.00 0.86 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00 Asp Cys
++0.001900 5.53 -0.594 0.266 -0.998 -0.224 7.50 0.01 0.50 13.700 3.630 6.54 -0.11 0.34 1 0.00 0.00 0.00 0.00 0.50 0.00 1.50 0.00 0.50 0.00 0.0000 0.00 2.53 3.29 0.00 0.00 0.00 1.24 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00 Asp Met
++0.000880 6.23 -0.445 0.162 -0.998 -0.255 5.30 0.01 0.56 13.700 3.810 6.86 -0.07 0.31 1 0.00 0.00 0.00 0.00 0.50 0.00 1.50 0.00 0.50 0.00 0.0000 0.00 2.08 2.99 0.00 0.00 0.00 1.25 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00 Asp Phe
++0.002780 6.15 -0.232 0.249 -0.998 0.356 7.40 0.00 0.55 13.700 3.580 6.45 -0.05 0.13 1 0.00 0.00 0.00 0.00 0.50 0.00 1.50 0.00 0.50 0.00 0.0000 0.00 2.68 3.54 0.00 0.00 0.00 1.30 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00 Asp Ile
++0.002780 6.15 -0.232 0.249 -0.998 0.356 7.40 0.00 0.55 13.700 3.580 6.45 -0.05 0.13 1 0.00 0.00 0.00 0.00 0.50 0.00 1.50 0.00 0.50 0.00 0.0000 0.00 2.68 3.54 0.00 0.00 0.00 1.30 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00 Asp Leu
++0.000480 7.27 -0.152 0.069 -0.998 0.084 7.60 0.69 0.87 13.600 3.880 6.99 0.01 0.08 1 0.00 0.00 0.00 0.00 0.50 0.00 1.50 0.00 0.50 0.00 0.0000 0.00 0.42 2.19 0.00 0.00 0.00 1.10 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00 Asp Val
++0.000100 6.89 0.100 -0.556 -0.998 -0.599 5.30 0.01 0.47 13.700 4.000 7.21 0.37 -0.15 1 0.00 0.00 0.00 0.00 1.50 0.00 0.50 0.00 0.50 0.00 0.0000 0.00 0.56 2.36 0.00 0.00 0.00 1.11 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00 Asp Trp
++0.000010 8.99 -0.088 0.136 -0.998 -0.113 0.00 0.11 2.06 4.800 3.100 5.82 0.12 0.06 1 0.00 0.00 0.00 0.00 0.50 0.00 0.60 0.00 0.50 0.00 0.0100 4.69 3.02 4.02 0.00 0.89 0.00 0.06 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00 Asp Tyr
++0.000160 7.24 -0.166 0.136 -0.998 0.102 7.50 0.61 0.84 13.700 3.540 6.38 0.01 0.11 1 0.00 0.00 0.00 0.00 0.50 0.00 1.50 0.00 0.50 0.00 0.0000 0.00 2.16 3.14 0.00 0.00 0.00 1.02 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00 Asp Ala
++0.000140 6.95 -0.138 -0.017 -0.998 -0.047 7.50 0.62 0.81 13.700 3.320 5.98 0.06 0.02 1 0.00 0.00 0.00 0.00 0.50 0.00 1.50 0.00 0.50 0.00 0.0000 0.00 0.29 2.29 0.00 0.00 0.00 0.75 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00 Asp Gly
++0.003760 5.73 -0.054 0.189 -0.998 0.123 0.70 4.70 4.04 4.500 3.490 6.88 0.08 0.09 1 0.00 0.00 0.00 0.00 0.60 0.00 0.50 0.00 0.00 0.50 0.0100 3.18 3.05 3.82 1.69 1.18 0.00 0.10 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00 Asp Thr
++0.000090 7.65 -0.019 0.123 -0.998 0.039 0.90 4.69 4.14 4.500 3.290 6.18 0.10 0.10 1 0.00 0.00 0.00 0.00 0.50 0.00 0.60 0.00 0.50 0.00 0.0100 2.81 2.25 3.47 0.00 0.97 0.00 0.75 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00 Asp Ser
++0.002110 5.89 -0.026 0.246 -0.998 0.156 0.60 4.56 4.19 4.500 3.520 6.61 0.03 0.10 1 0.00 0.00 0.00 0.00 0.50 0.00 0.60 0.00 0.50 0.00 0.0100 4.07 3.04 4.03 0.10 1.00 0.00 0.32 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00 Asp Gln
++0.002910 5.53 0.030 0.199 -0.998 0.091 0.60 4.54 4.20 4.500 3.290 6.18 0.12 0.16 1 0.00 0.00 0.00 0.00 0.50 0.00 0.60 0.00 0.50 0.00 0.0100 2.90 2.05 3.03 0.16 1.08 0.00 0.35 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00 Asp Asn
++0.917000 3.97 0.083 0.059 0.992 0.395 6.40 0.37 0.63 13.700 3.500 6.30 0.48 -0.09 1 0.00 0.00 0.00 0.00 0.50 0.00 0.50 0.00 0.50 0.60 0.0001 4.99 4.37 0.68 0.00 0.00 0.00 0.04 0.64 79.70 51.20 34.50 4.60 0.61 0.69 1.00 Asp Glu
++0.000002 5.55 -0.279 -0.279 -0.990 -0.990 0.07 -62.40 6.29 13.000 4.440 4.44 0.07 0.07 1 0.00 0.00 0.00 0.00 0.50 0.00 0.50 0.00 0.50 0.50 0.0009 5.00 0.34 0.34 0.00 0.00 0.00 0.94 0.94 13.20 -13.80 1.30 33.30 9.29 9.29 1.00 Asp Asp
++0.001290 5.56 0.002 0.216 -0.997 0.024 0.20 2.50 3.50 4.600 3.610 6.78 0.00 0.13 1 0.00 0.00 0.00 0.00 0.60 0.00 0.60 0.00 0.00 0.00 0.0000 0.00 0.00 0.00 0.43 179.42 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00 His Cys
++0.000850 5.67 0.081 0.294 -0.998 0.160 0.01 4.05 4.65 4.320 4.090 7.70 -0.09 -0.04 1 0.00 0.00 0.00 0.00 0.60 0.00 1.50 0.00 0.00 0.00 0.0000 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00 His Met
++0.001020 5.55 0.100 0.299 -0.998 0.325 0.30 3.44 3.76 4.300 4.410 8.28 -0.15 -0.00 1 0.00 0.00 0.00 0.00 0.60 0.00 1.50 0.00 0.00 0.00 0.0000 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00 His Phe
++0.001220 6.16 0.070 0.230 -0.998 0.209 0.40 4.16 4.58 4.400 3.960 7.43 0.02 -0.00 1 0.00 0.00 0.00 0.00 0.60 0.00 1.50 0.00 0.00 0.00 0.0000 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00 His Ile
++0.001220 6.16 0.070 0.230 -0.998 0.209 0.40 4.16 4.58 4.400 3.960 7.43 0.02 -0.00 1 0.00 0.00 0.00 0.00 0.60 0.00 1.50 0.00 0.00 0.00 0.0000 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00 His Leu
++0.000090 7.81 0.045 0.068 -0.998 0.034 0.60 4.52 4.18 4.300 4.030 7.57 0.05 0.03 1 0.00 0.00 0.00 0.00 0.60 0.00 1.50 0.00 0.00 0.00 0.0000 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00 His Val
++0.000090 7.00 0.073 0.168 -0.998 0.190 0.70 3.48 3.67 4.300 4.220 7.94 -0.26 -0.36 1 0.00 0.00 0.00 0.00 1.50 0.00 0.60 0.00 0.00 0.00 0.0000 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00 His Trp
++0.000100 6.94 0.081 0.185 -0.997 0.218 0.40 4.53 4.12 4.000 4.690 8.82 -0.10 -0.18 1 0.00 0.00 0.00 0.00 0.60 0.00 0.60 0.00 0.00 0.00 0.0000 0.00 0.00 0.00 0.57 179.48 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00 His Tyr
++0.000800 5.68 0.089 0.150 -0.998 0.072 0.20 4.18 4.28 4.400 3.770 7.10 0.13 -0.07 1 0.00 0.00 0.00 0.00 0.60 0.00 1.50 0.00 0.00 0.00 0.0000 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00 His Ala
++0.000010 7.62 0.055 -0.036 -0.998 -0.147 0.00 2.61 3.66 4.700 3.100 5.84 0.21 -0.01 1 0.00 0.00 0.00 0.00 0.60 0.00 1.50 0.00 0.00 0.00 0.0000 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00 His Gly
++0.000130 7.16 -0.032 0.152 -0.997 -0.015 0.20 4.41 4.35 4.400 3.860 7.26 0.13 0.01 1 0.00 0.00 0.00 0.00 0.60 0.00 0.60 0.00 0.00 0.00 0.0000 0.00 0.00 0.00 0.87 179.40 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00 His Thr
++0.002080 5.36 -0.005 0.235 -0.997 0.162 0.00 4.06 4.30 4.400 3.770 7.08 0.01 0.03 1 0.00 0.00 0.00 0.00 0.60 0.00 0.60 0.00 0.00 0.00 0.0000 0.00 0.00 0.00 0.39 179.42 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00 His Ser
++0.000090 7.27 0.069 0.144 -0.997 0.055 0.30 4.50 4.32 4.200 4.250 7.99 0.02 -0.04 1 0.00 0.00 0.00 0.00 0.60 0.00 0.60 0.00 0.00 0.00 0.0000 0.00 0.00 0.00 0.22 179.45 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00 His Gln
++0.000100 6.92 0.024 0.159 -0.997 0.021 0.00 2.12 3.57 4.700 3.450 6.49 0.10 0.12 1 0.00 0.00 0.00 0.00 0.60 0.00 0.60 0.00 0.00 0.00 0.0000 0.00 0.00 0.00 0.04 179.45 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00 His Asn
++0.000090 7.80 0.005 0.160 -0.998 0.080 0.60 4.63 4.07 4.300 4.010 7.54 -0.10 0.06 1 0.00 0.00 0.00 0.00 0.50 0.00 0.60 0.00 0.60 0.00 0.0100 2.57 1.15 2.08 0.00 1.07 0.00 0.30 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00 His Glu
++0.000090 7.67 -0.043 0.153 -0.998 0.017 0.50 4.59 4.11 4.400 3.660 6.87 0.04 0.03 1 0.00 0.00 0.00 0.00 0.50 0.00 0.60 0.00 0.50 0.00 0.0100 2.61 1.09 2.05 0.00 1.08 0.00 0.03 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00 His Asp
++0.000190 6.60 0.139 0.139 -0.155 -0.155 0.40 4.17 3.38 32.100 8.020 8.02 -0.03 -0.03 1 0.00 0.00 0.00 0.00 0.60 0.00 0.60 0.00 0.00 0.00 0.0000 0.00 0.00 0.00 0.08 183.37 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00 His His
++0.000130 6.65 0.137 0.134 -0.998 0.129 0.20 4.39 4.16 4.200 4.220 7.94 0.06 -0.11 1 0.00 0.00 0.00 0.00 0.80 0.00 0.60 0.00 0.30 0.00 0.0100 2.97 1.02 2.01 0.00 1.46 0.00 0.10 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00 Arg Cys
++0.000020 7.83 -0.131 0.130 -0.998 -0.346 7.60 0.11 0.35 13.400 5.360 9.66 -0.11 -0.05 1 0.00 0.00 0.00 0.00 0.80 0.00 1.50 0.00 0.30 0.00 0.0000 0.00 4.28 4.87 0.00 0.00 0.00 0.10 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00 Arg Met
++0.000010 7.50 0.105 0.161 -0.998 0.244 7.90 0.13 0.43 13.500 4.500 8.12 -0.08 -0.08 1 0.00 0.00 0.00 0.00 0.80 0.00 1.50 0.00 0.30 0.00 0.0000 0.00 0.53 2.18 0.00 0.00 0.00 0.01 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00 Arg Phe
++0.000070 7.74 0.112 0.143 -0.998 0.355 7.60 0.25 0.46 13.500 5.160 9.30 0.02 -0.09 1 0.00 0.00 0.00 0.00 0.80 0.00 1.50 0.00 0.30 0.00 0.0000 0.00 0.53 2.18 0.00 0.00 0.00 0.08 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00 Arg Ile
++0.000070 7.74 0.112 0.143 -0.998 0.355 7.60 0.25 0.46 13.500 5.160 9.30 0.02 -0.09 1 0.00 0.00 0.00 0.00 0.80 0.00 1.50 0.00 0.30 0.00 0.0000 0.00 0.53 2.18 0.00 0.00 0.00 0.08 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00 Arg Leu
++0.000060 5.57 0.162 0.068 -0.998 0.115 7.50 0.23 0.49 13.600 4.460 8.04 0.16 -0.02 1 0.00 0.00 0.00 0.00 0.80 0.00 1.50 0.00 0.30 0.00 0.0000 0.00 0.53 2.18 0.00 0.00 0.00 0.09 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00 Arg Val
++0.000050 7.01 0.023 0.151 -0.998 -0.001 8.00 0.38 0.66 13.600 4.160 7.51 -0.07 0.06 1 0.00 0.00 0.00 0.00 1.50 0.00 0.80 0.00 0.00 0.30 0.0000 0.00 4.46 5.02 0.00 0.00 0.00 0.04 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00 Arg Trp
++0.000100 6.42 0.154 0.087 -0.998 0.060 0.70 4.15 4.36 4.300 3.950 7.43 0.04 -0.05 1 0.00 0.00 0.00 0.00 0.80 0.00 0.60 0.00 0.30 0.00 0.0100 3.28 1.01 2.00 0.09 3.42 0.00 0.02 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00 Arg Tyr
++0.000060 6.86 0.122 0.083 -0.998 0.396 7.80 0.08 0.35 13.500 4.780 8.61 0.03 -0.22 1 0.00 0.00 0.00 0.00 0.80 0.00 1.50 0.00 0.30 0.00 0.0000 0.00 0.28 2.13 0.00 0.00 0.00 0.59 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00 Arg Ala
++0.000020 7.15 0.141 -0.060 -0.998 -0.259 7.10 0.05 0.35 13.600 4.150 7.48 0.18 -0.03 1 0.00 0.00 0.00 0.00 0.80 0.00 1.50 0.00 0.30 0.00 0.0000 0.00 0.39 2.15 0.00 0.00 0.00 0.59 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00 Arg Gly
++0.000020 8.07 0.115 0.098 -0.998 0.071 4.10 0.00 0.52 13.700 4.450 8.37 0.11 0.03 1 0.00 0.00 0.00 0.00 0.80 0.00 0.60 0.00 0.30 0.00 0.0100 3.12 0.60 2.20 0.11 1.63 0.00 0.12 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00 Arg Thr
++0.000130 6.50 0.145 0.153 -0.998 0.172 0.20 4.27 4.26 4.300 4.010 7.54 0.05 -0.18 1 0.00 0.00 0.00 0.00 0.80 0.00 0.60 0.00 0.30 0.00 0.0100 2.86 1.05 2.02 0.00 1.47 0.00 0.04 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00 Arg Ser
++0.000230 6.64 0.106 0.227 -0.998 0.340 0.50 4.42 4.15 4.200 4.390 8.25 0.03 -0.09 1 0.00 0.00 0.00 0.00 0.80 0.00 0.60 0.00 0.30 0.00 0.0100 3.10 1.01 2.01 0.00 1.58 0.00 0.10 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00 Arg Gln
++0.000020 8.02 0.086 0.134 -0.998 0.183 3.50 0.00 0.52 13.600 5.250 8.62 0.06 -0.14 1 0.00 0.00 0.00 0.00 0.80 0.00 0.60 0.00 0.30 0.00 0.0100 2.78 0.71 2.23 0.09 1.86 0.00 0.06 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00 Arg Asn
++0.080000 4.17 -0.279 0.227 0.000 0.000 14.67 -0.07 0.29 13.210 3.290 6.00 0.43 -0.99 4 1.24 0.47 1.00 0.00 0.50 1.84 0.10 2.27 0.83 0.03 0.0100 5.74 3.34 2.51 0.00 0.00 39.77 1.55 1.34 0.15 0.15 0.15 16.38 4.00 7.79 2.28 Arg Glu
++0.010000 3.52 -0.924 0.050 0.000 0.000 9.53 -0.16 0.34 13.600 3.220 5.86 0.05 0.66 4 1.16 0.18 1.00 0.00 0.14 1.40 0.20 2.35 0.53 0.13 0.0100 5.54 2.00 3.72 0.00 0.00 18.31 1.62 1.50 1.00 1.00 1.00 34.01 4.00 8.29 2.32 Arg Asp
++0.000210 6.21 0.134 0.215 -0.998 0.320 0.40 4.43 4.11 4.100 4.450 8.36 0.03 -0.04 1 0.00 0.00 0.00 0.00 0.80 0.00 0.60 0.00 0.30 0.00 0.0100 3.03 1.01 2.00 0.00 1.75 0.00 0.04 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00 Arg His
++0.000020 7.58 0.146 0.146 -0.107 -0.107 1.10 2.58 2.63 33.000 6.470 6.47 0.17 0.17 1 0.00 0.00 0.00 0.00 0.80 0.00 0.80 0.00 0.30 0.30 0.0100 3.18 0.41 0.41 0.00 0.00 0.00 0.01 0.01 87.60 64.00 36.70 21.20 1.21 1.21 1.00 Arg Arg
++0.001410 6.11 0.119 0.163 -0.998 0.230 0.30 4.11 4.58 4.500 3.580 6.72 -0.15 -0.02 1 0.00 0.00 0.00 0.00 1.00 0.00 0.60 0.00 0.70 0.00 0.0100 2.95 0.98 1.99 0.04 1.16 0.00 0.40 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00 Lys Cys
++0.033790 4.81 -0.206 -0.152 -0.998 -0.566 8.20 0.15 0.38 13.400 10.260 5.73 -1.00 -0.66 1 0.00 0.00 0.00 0.00 1.00 0.00 1.50 0.00 0.70 0.00 0.0000 0.00 2.41 0.17 0.00 0.00 0.00 0.94 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00 Lys Met
++0.000010 7.98 0.002 0.125 -0.998 0.067 8.90 0.05 0.34 13.400 4.880 8.80 -0.33 -0.13 1 0.00 0.00 0.00 0.00 1.00 0.00 1.50 0.00 0.70 0.00 0.0000 0.00 0.16 2.12 0.00 0.00 0.00 0.71 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00 Lys Phe
++0.002330 6.22 -0.072 0.206 -0.998 0.353 7.70 0.00 0.48 13.600 3.920 7.07 -0.16 0.03 1 0.00 0.00 0.00 0.00 1.00 0.00 1.50 0.00 0.70 0.00 0.0000 0.00 0.56 2.18 0.00 0.00 0.00 1.06 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00 Lys Ile
++0.002330 6.22 -0.072 0.206 -0.998 0.353 7.70 0.00 0.48 13.600 3.920 7.07 -0.16 0.03 1 0.00 0.00 0.00 0.00 1.00 0.00 1.50 0.00 0.70 0.00 0.0000 0.00 0.56 2.18 0.00 0.00 0.00 1.06 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00 Lys Leu
++0.001250 6.46 -0.030 -0.062 -0.998 0.096 7.70 0.00 0.47 13.600 3.900 7.03 -0.09 0.01 1 0.00 0.00 0.00 0.00 1.00 0.00 1.50 0.00 0.70 0.00 0.0000 0.00 0.50 2.17 0.00 0.00 0.00 1.03 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00 Lys Val
++0.253010 3.82 0.150 0.296 -0.998 0.997 9.00 0.11 0.46 13.600 3.830 6.91 -1.00 -0.14 1 0.00 0.00 0.00 0.00 1.50 0.00 1.00 0.00 0.00 0.70 0.0000 0.00 4.46 5.01 0.00 0.00 0.00 0.02 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00 Lys Trp
++0.000040 7.14 0.131 0.202 -0.998 0.223 0.60 4.37 4.26 4.200 4.300 8.08 -0.25 0.00 1 0.00 0.00 0.00 0.00 1.00 0.00 0.60 0.00 0.70 0.00 0.0100 3.07 1.00 1.20 1.10 1.72 0.00 0.04 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00 Lys Tyr
++0.000100 7.30 -0.080 0.120 -0.998 0.263 7.70 0.24 0.53 13.600 4.070 7.34 -0.17 -0.05 1 0.00 0.00 0.00 0.00 1.00 0.00 1.50 0.00 0.70 0.00 0.0000 0.00 0.37 2.14 0.00 0.00 0.00 0.88 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00 Lys Ala
++0.000060 6.25 -0.065 -0.056 -0.998 -0.161 7.50 0.26 0.53 13.600 3.770 6.80 -0.03 0.02 1 0.00 0.00 0.00 0.00 1.00 0.00 1.50 0.00 0.70 0.00 0.0000 0.00 0.22 2.12 0.00 0.00 0.00 0.80 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00 Lys Gly
++0.033500 4.96 -0.054 0.072 -0.998 -0.373 0.01 1.98 4.82 4.800 3.070 5.77 -0.07 -1.00 1 0.00 0.00 0.00 0.00 0.60 0.00 1.00 0.00 0.00 0.70 0.0100 2.98 3.51 3.88 0.00 1.79 0.00 1.06 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00 Lys Thr
++0.001460 5.63 0.160 0.217 -0.998 0.235 0.20 4.05 4.62 4.500 3.550 6.68 0.20 -0.04 1 0.00 0.00 0.00 0.00 1.00 0.00 0.60 0.00 0.70 0.00 0.0100 2.97 0.98 1.99 0.02 1.17 0.00 0.68 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00 Lys Ser
++0.000040 8.12 0.097 0.149 -0.998 0.225 0.30 4.03 4.66 4.400 3.730 7.01 -0.07 -0.03 1 0.00 0.00 0.00 0.00 1.00 0.00 0.60 0.00 0.70 0.00 0.0100 2.78 1.40 2.23 3.29 1.23 0.00 0.72 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00 Lys Gln
++0.000060 7.64 0.122 0.151 -0.998 0.182 0.40 4.15 4.37 4.400 3.840 7.21 -0.05 -0.12 1 0.00 0.00 0.00 0.00 1.00 0.00 0.60 0.00 0.70 0.00 0.0100 3.46 4.83 5.09 3.02 2.50 0.00 1.16 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00 Lys Asn
++0.010000 5.49 -0.859 0.200 0.000 0.000 15.97 -0.01 0.35 13.040 3.730 6.79 0.01 0.23 4 0.20 1.41 1.00 0.00 1.30 2.25 0.20 2.25 1.13 0.13 0.0100 4.60 2.00 3.43 0.00 0.00 43.61 1.80 1.72 0.03 0.03 0.03 15.05 4.00 3.35 5.99 Lys Glu
++0.010000 5.14 0.071 0.131 0.000 0.000 7.26 0.19 0.63 13.700 3.150 5.68 0.20 -1.00 4 0.04 1.16 1.00 0.00 1.24 2.20 0.20 1.93 0.26 0.13 0.0100 4.15 2.00 3.66 0.00 0.00 26.41 1.99 1.34 0.04 0.04 0.04 14.60 4.00 5.28 8.92 Lys Asp
++0.000010 8.29 0.113 0.117 -0.998 0.018 0.04 4.63 3.97 4.100 4.060 8.65 -0.14 0.04 1 0.00 0.00 0.00 0.00 1.00 0.00 0.60 0.00 0.70 0.00 0.0100 3.34 0.98 1.99 3.36 2.08 0.00 0.04 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00 Lys His
++1.460000 3.67 0.158 0.009 0.381 -0.036 7.20 0.02 0.45 13.600 4.140 7.47 0.01 0.05 1 0.00 0.00 0.00 0.00 1.00 0.00 0.80 0.00 0.70 0.30 0.0070 4.00 4.38 0.70 0.00 0.00 0.00 0.01 0.05 79.70 51.20 34.50 4.60 0.69 0.78 1.00 Lys Arg
++0.000540 5.58 0.397 0.397 0.257 0.257 0.80 -0.19 3.81 33.000 5.130 5.13 -0.16 -0.16 1 0.00 0.00 0.00 0.00 1.00 0.00 1.00 0.00 0.70 0.70 0.0001 3.00 2.11 2.11 0.00 0.00 0.00 0.01 0.01 87.60 64.00 36.70 21.20 2.51 2.51 1.00 Lys Lys
++0.003210 5.65 0.065 0.188 -0.670 0.121 0.80 4.47 4.32 4.500 3.430 6.44 0.06 0.09 1 0.00 0.00 0.00 0.00 0.60 0.00 1.50 0.00 0.00 0.00 0.0000 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00 Pro Cys
++0.176000 4.08 0.343 0.456 0.464 -0.390 4.90 0.59 0.67 31.600 5.460 7.58 0.20 0.14 1 0.00 0.00 0.00 0.00 2.50 0.00 2.50 0.00 0.00 0.00 0.0000 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00 Pro Met
++0.014000 4.81 0.476 0.462 0.955 0.408 9.80 0.07 0.31 32.900 6.360 8.01 0.09 0.04 1 0.00 0.00 0.00 0.00 2.50 0.00 2.50 0.00 0.00 0.00 0.0000 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00 Pro Phe
++0.005600 5.93 0.219 0.215 0.181 0.556 37.00 -0.06 0.24 31.300 5.460 7.58 0.12 0.00 1 0.00 0.00 0.00 0.00 2.50 0.00 2.50 0.00 0.00 0.00 0.0000 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00 Pro Ile
++0.005600 5.93 0.219 0.215 0.181 0.556 37.00 -0.06 0.24 31.300 5.460 7.58 0.12 0.00 1 0.00 0.00 0.00 0.00 2.50 0.00 2.50 0.00 0.00 0.00 0.0000 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00 Pro Leu
++0.093400 4.73 0.407 0.079 0.663 -0.564 5.60 0.99 0.97 33.100 5.160 7.16 0.21 0.03 1 0.00 0.00 0.00 0.00 2.50 0.00 2.50 0.00 0.00 0.00 0.0000 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00 Pro Val
++0.015700 4.58 0.500 0.534 0.998 0.507 22.30 -0.12 0.21 9.600 4.610 7.83 0.02 0.09 1 0.00 0.00 0.00 0.00 2.50 0.00 2.50 0.00 0.00 0.00 0.0000 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00 Pro Trp
++0.000530 6.04 0.120 0.163 -0.998 0.128 0.50 3.56 3.71 4.300 4.270 8.03 -0.07 -0.05 1 0.00 0.00 0.00 0.00 0.60 0.00 1.50 0.00 0.00 0.00 0.0000 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00 Pro Tyr
++0.005200 5.36 0.127 0.127 0.318 -0.390 17.00 0.14 0.37 31.300 5.080 7.06 0.04 0.39 1 0.00 0.00 0.00 0.00 2.50 0.00 2.50 0.00 0.00 0.00 0.0000 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00 Pro Ala
++0.000040 7.83 0.030 -0.008 -0.997 -0.042 36.90 -0.05 0.27 31.300 4.560 6.33 0.18 -0.04 1 0.00 0.00 0.00 0.00 2.50 0.00 2.50 0.00 0.00 0.00 0.0000 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00 Pro Gly
++0.004450 5.78 0.036 0.196 -0.813 0.185 0.90 4.56 4.23 4.500 3.480 6.55 0.13 0.10 1 0.00 0.00 0.00 0.00 0.60 0.00 1.50 0.00 0.00 0.00 0.0000 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00 Pro Thr
++0.004800 5.46 0.089 0.192 -0.581 0.115 0.90 4.64 4.16 4.500 3.370 6.33 0.12 0.11 1 0.00 0.00 0.00 0.00 0.60 0.00 1.50 0.00 0.00 0.00 0.0000 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00 Pro Ser
++0.001100 6.18 0.101 0.172 -0.998 0.214 0.60 4.36 4.48 4.500 3.610 6.80 0.10 0.03 1 0.00 0.00 0.00 0.00 0.60 0.00 1.50 0.00 0.00 0.00 0.0000 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00 Pro Gln
++0.002220 5.73 0.102 0.153 -0.607 0.025 0.70 4.62 4.12 4.400 3.660 6.89 0.12 0.05 1 0.00 0.00 0.00 0.00 0.60 0.00 1.50 0.00 0.00 0.00 0.0000 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00 Pro Asn
++0.000550 6.84 -0.157 0.154 -0.998 0.202 7.60 0.55 0.78 13.600 3.940 7.11 -0.12 0.08 1 0.00 0.00 0.00 0.00 0.50 0.00 1.50 0.00 0.60 0.00 0.0000 0.00 2.03 2.93 0.00 0.00 0.00 1.09 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00 Pro Glu
++0.000280 7.13 -0.171 0.143 -0.998 0.134 7.60 0.60 0.80 13.600 3.780 6.81 -0.01 0.11 1 0.00 0.00 0.00 0.00 0.50 0.00 1.50 0.00 0.50 0.00 0.0000 0.00 0.79 2.29 0.00 0.00 0.00 0.98 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00 Pro Asp
++0.000070 7.49 0.046 0.113 -0.998 0.012 0.60 3.57 3.73 4.400 3.860 7.25 0.09 -0.01 1 0.00 0.00 0.00 0.00 0.60 0.00 1.50 0.00 0.00 0.00 0.0000 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00 Pro His
++0.000040 7.60 0.141 0.137 -0.998 0.314 7.70 0.17 0.44 13.600 4.440 8.00 0.06 -0.08 1 0.00 0.00 0.00 0.00 0.80 0.00 1.50 0.00 0.30 0.00 0.0000 0.00 0.52 2.18 0.00 0.00 0.00 0.06 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00 Pro Arg
++0.000200 7.26 0.124 0.251 -0.998 -0.143 7.80 0.26 0.55 13.600 4.220 7.61 -0.14 -0.00 1 0.00 0.00 0.00 0.00 1.00 0.00 1.50 0.00 0.70 0.00 0.0000 0.00 0.26 2.12 0.00 0.00 0.00 0.95 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00 Pro Lys
++0.010200 4.71 0.349 0.349 0.535 0.535 49.90 -0.53 0.47 5.710 7.810 7.81 0.17 0.17 1 0.00 0.00 0.00 0.00 2.50 0.00 2.50 0.00 0.00 0.00 0.0000 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00 Pro Pro
--- /dev/null
--- /dev/null
++1.1970470 5.3667307 0 0 0 0 3.0000000
++1.5539975 5.6438808 0 0 0 0 3.0000000
++1.6679316 5.6689787 0 0 0 0 3.0000000
++1.6606077 5.9381499 0 0 0 0 3.0000000
++1.7428987 5.8625088 0 0 0 0 3.0000000
++1.7310307 5.9950466 0 0 0 0 3.0000000
++1.6322831 5.8318806 0 0 0 0 3.0000000
++1.5348705 5.4955850 0 0 0 0 3.0000000
++1.3603992 5.3937664 0 0 0 0 3.0000000
++1.3228511 5.4371481 0 0 0 0 3.0000000
++1.1970470 5.3667307 0 0 0 0 3.0000000
++1.0325602 5.5439558 0 0 0 0 3.0000000
++0.98513186 5.3780737 0 0 0 0 3.0000000
++0.97556829 5.3995867 0 0 0 0 3.0000000
++0.90197319 5.4184709 0 0 0 0 3.0000000
++0.77024281 5.4679136 0 0 0 0 3.0000000
++0.75456488 5.4686551 0 0 0 0 3.0000000
++1.1983876 5.3466215 0 0 0 0 3.0000000
++0.96779823 5.2968884 0 0 0 0 3.0000000
++0.92065424 5.3752089 0 0 0 0 3.0000000
++1.1218165 5.6721835 0 0 0 0 3.0000000
++1.6679316 5.7029562 0 0 0 0 3.0000000
++1.6606077 5.9355397 0 0 0 0 3.0000000
++1.3228511 5.4343948 0 0 0 0 3.0000000
++1.3228511 5.4343948 0 0 0 0 3.0000000
++ 0.000 0.000 0.000 0.000 0.000 0.000E+00 0.00 ! Pro
++ 0.000 0.000 0.000 0.000 0.000 0.000E+00 0.00 ! Pro
++ 0.000 0.000 0.000 0.000 0.000 0.000E+00 0.00 ! Pro
++ 0.000 0.000 0.000 0.000 0.000 0.000E+00 0.00 ! Pro
++ 0.000 0.000 0.000 0.000 0.000 0.000E+00 0.00 ! Pro
++ 0.000 0.000 0.000 0.000 0.000 0.000E+00 0.00 ! Pro
++ 0.000 0.000 0.000 0.000 0.000 0.000E+00 0.00 ! Pro
++
use control_data, only: titel,outpdb,outmol2,refstr,pdbref,&
iscode,symetr,punch_dist,print_dist,nstart,nend,&
caonly,iopt,efree,lprint_cart,lprint_int,rlamb_ele,&
- r_cut_ele,nclust,tor_mode,scelemode,constr_dist
+ r_cut_ele,nclust,tor_mode,scelemode,r_cut_mart,r_cut_ang,&
- rlamb_mart
++ rlamb_mart,constr_dist
+ use geometry_data, only:bordliptop,bordlipbot,&
+ bufliptop,buflipbot,lipthick,lipbufthick
! implicit none
! include 'DIMENSIONS'
! include 'sizesclu.dat'
set (CMAKE_Fortran_FLAGS_RELEASE " ")
set (CMAKE_Fortran_FLAGS_DEBUG "-O0 -g -traceback")
# set(FFLAGS0 "-fpp -c -CB -g -ip " )
-- set(FFLAGS0 "-O3 -ip -fpp -heap-arrays -mcmodel=medium" )
++ set(FFLAGS0 "-CB -g -ip -fpp -heap-arrays -mcmodel=large" )
# set(FFLAGS0 "-O0 -CB -CA -g" )
set(FFLAGS1 "-fpp -c -O " )
set(FFLAGS2 "-fpp -c -g -CA -CB ")
end subroutine gauss
!-----------------------------------------------------------------------------
! kinetic_lesyng.f
++#ifdef FIVEDIAG
++ subroutine kinetic(KE_total)
++!c----------------------------------------------------------------
++!c This subroutine calculates the total kinetic energy of the chain
++!c-----------------------------------------------------------------
++!c 3/5/2020 AL Corrected for multichain systems, no fake peptide groups
++!c inside, implemented with five-diagonal inertia matrix
++ implicit none
++ include 'DIMENSIONS'
++ include 'COMMON.VAR'
++ include 'COMMON.CHAIN'
++ include 'COMMON.DERIV'
++ include 'COMMON.GEO'
++ include 'COMMON.LOCAL'
++ include 'COMMON.INTERACT'
++ include 'COMMON.MD'
++ include 'COMMON.LAGRANGE.5diag'
++ include 'COMMON.IOUNITS'
++ double precision KE_total
++ integer i,j,k,iti
++ double precision KEt_p,KEt_sc,KEr_p,KEr_sc,incr(3),&
++ mag1,mag2,v(3)
++
++ KEt_p=0.0d0
++ KEt_sc=0.0d0
++ KEr_p=0.0D0
++ KEr_sc=0.0D0
++!c write (iout,*) "ISC",(isc(itype(i)),i=1,nres)
++!c The translational part for peptide virtual bonds
++ do j=1,3
++ incr(j)=d_t(j,0)
++ enddo
++ do i=nnt,nct-1
++!c write (iout,*) "Kinetic trp:",i,(incr(j),j=1,3
++!c Skip dummy peptide groups
++ if (itype(i).ne.ntyp1 .and. itype(i+1).ne.ntyp1) then
++ do j=1,3
++ v(j)=incr(j)+0.5d0*d_t(j,i)
++ enddo
++!c write (iout,*) "Kinetic trp:",i,(v(j),j=1,3)
++ vtot(i)=v(1)*v(1)+v(2)*v(2)+v(3)*v(3)
++ KEt_p=KEt_p+(v(1)*v(1)+v(2)*v(2)+v(3)*v(3))
++ endif
++ do j=1,3
++ incr(j)=incr(j)+d_t(j,i)
++ enddo
++ enddo
++!c write(iout,*) 'KEt_p', KEt_p
++!c The translational part for the side chain virtual bond
++!c Only now we can initialize incr with zeros. It must be equal
++!c to the velocities of the first Calpha.
++ do j=1,3
++ incr(j)=d_t(j,0)
++ enddo
++ do i=nnt,nct
++ iti=iabs(itype(i))
++ if (itype(i).eq.10 .and. itype(i).ne.ntyp1) then
++ do j=1,3
++ v(j)=incr(j)
++ enddo
++ else
++ do j=1,3
++ v(j)=incr(j)+d_t(j,nres+i)
++ enddo
++ endif
++!c write (iout,*) "Kinetic trsc:",i,(incr(j),j=1,3)
++!c write (iout,*) "i",i," msc",msc(iti)," v",(v(j),j=1,3)
++ KEt_sc=KEt_sc+msc(iti)*(v(1)*v(1)+v(2)*v(2)+v(3)*v(3))
++ vtot(i+nres)=v(1)*v(1)+v(2)*v(2)+v(3)*v(3)
++ do j=1,3
++ incr(j)=incr(j)+d_t(j,i)
++ enddo
++ enddo
++! goto 111
++! write(iout,*) 'KEt_sc', KEt_sc
++! The part due to stretching and rotation of the peptide groups
++ do i=nnt,nct-1
++ if (itype(i).ne.ntyp1.and.itype(i+1).ne.ntyp1) then
++! write (iout,*) "i",i
++! write (iout,*) "i",i," mag1",mag1," mag2",mag2
++ do j=1,3
++ incr(j)=d_t(j,i)
++ enddo
++!c write (iout,*) "Kinetic rotp:",i,(incr(j),j=1,3)
++ KEr_p=KEr_p+(incr(1)*incr(1)+incr(2)*incr(2) &
++ +incr(3)*incr(3))
++ endif
++ enddo
++!c goto 111
++!c write(iout,*) 'KEr_p', KEr_p
++!c The rotational part of the side chain virtual bond
++ do i=nnt,nct
++ iti=iabs(itype(i))
++ if (itype(i).ne.10.and.itype(i).ne.ntyp1) then
++ do j=1,3
++ incr(j)=d_t(j,nres+i)
++ enddo
++!c write (iout,*) "Kinetic rotsc:",i,(incr(j),j=1,3)
++ KEr_sc=KEr_sc+Isc(iti)*(incr(1)*incr(1)+incr(2)*incr(2)+&
++ incr(3)*incr(3))
++ endif
++ enddo
++!c The total kinetic energy
++ 111 continue
++!c write(iout,*) ' KEt_p',KEt_p,' KEt_sc',KEt_sc,' KEr_p',KEr_p,
++!c & ' KEr_sc', KEr_sc
++ KE_total=0.5d0*(mp*KEt_p+KEt_sc+0.25d0*Ip*KEr_p+KEr_sc)
++!c write (iout,*) "KE_total",KE_total
++ return
++ end subroutine kinetic
++#else
++
!-----------------------------------------------------------------------------
subroutine kinetic(KE_total)
!----------------------------------------------------------------
do j=1,3
incr(j)=d_t(j,0)
enddo
- do i=nnt,nct-1
+ term=nct-1
+! if (molnum(nct).gt.3) term=nct
+ do i=nnt,term
mnum=molnum(i)
- if (mnum.eq.5) mp(mnum)=msc(itype(i,mnum),mnum)
-! write (iout,*) "Kinetic trp:",i,(incr(j),j=1,3)
+ if (mnum.ge.5) mp(mnum)=msc(itype(i,mnum),mnum)
+! write (iout,*) "Kinetic trp:",i,(incr(j),j=1,3),mp(mnum)
+ if (mnum.gt.4) then
do j=1,3
- v(j)=incr(j)+d_t(j,i)
+ v(j)=incr(j)+0.5d0*d_t(j,i)
- enddo
+ enddo
+ else
+ do j=1,3
+ v(j)=incr(j)+0.5d0*d_t(j,i)
+ enddo
+ endif
vtot(i)=v(1)*v(1)+v(2)*v(2)+v(3)*v(3)
KEt_p=KEt_p+mp(mnum)*(v(1)*v(1)+v(2)*v(2)+v(3)*v(3))
do j=1,3
return
end subroutine kinetic
!-----------------------------------------------------------------------------
++#endif
++ subroutine kinetic_CASC(KE_total)
++!c----------------------------------------------------------------
++!c Compute the kinetic energy of the system using the Calpha-SC
++!c coordinate system
++!c-----------------------------------------------------------------
++ implicit none
++ double precision KE_total
++
++ integer i,j,k,iti,ichain,innt,inct
++ double precision KEt_p,KEt_sc,KEr_p,KEr_sc,incr(3),&
++ mag1,mag2,v(3)
++#ifdef FIVEDIAG
++ KEt_p=0.0d0
++ KEt_sc=0.0d0
++ KEr_p=0.0D0
++ KEr_sc=0.0D0
++!c write (iout,*) "ISC",(isc(itype(i)),i=1,nres)
++!c The translational part for peptide virtual bonds
++ do ichain=1,nchain
++
++ innt=chain_border(1,ichain)
++ inct=chain_border(2,ichain)
++!c write (iout,*) "Kinetic_CASC chain",ichain," innt",innt,
++!c & " inct",inct
++
++ do i=innt,inct-1
++!c write (iout,*) i,(d_t(j,i),j=1,3),(d_t(j,i+1),j=1,3)
++ do j=1,3
++ v(j)=0.5d0*(d_t(j,i)+d_t(j,i+1))
++ enddo
++!c write (iout,*) "Kinetic trp i",i," v",(v(j),j=1,3)
++ KEt_p=KEt_p+(v(1)*v(1)+v(2)*v(2)+v(3)*v(3))
++ enddo
++!c write(iout,*) 'KEt_p', KEt_p
++!c The translational part for the side chain virtual bond
++!c Only now we can initialize incr with zeros. It must be equal
++!c to the velocities of the first Calpha.
++ do i=innt,inct
++ iti=iabs(itype(i))
++ if (iti.eq.10) then
++!c write (iout,*) i,iti,(d_t(j,i),j=1,3)
++ do j=1,3
++ v(j)=d_t(j,i)
++ enddo
++ else
++!c write (iout,*) i,iti,(d_t(j,nres+i),j=1,3)
++ do j=1,3
++ v(j)=d_t(j,nres+i)
++ enddo
++ endif
++!c write (iout,*) "Kinetic trsc:",i,(incr(j),j=1,3)
++!c write (iout,*) "i",i," msc",msc(iti)," v",(v(j),j=1,3)
++ KEt_sc=KEt_sc+msc(iti)*(v(1)*v(1)+v(2)*v(2)+v(3)*v(3))
++ enddo
++!c goto 111
++!c write(iout,*) 'KEt_sc', KEt_sc
++!c The part due to stretching and rotation of the peptide groups
++ do i=innt,inct-1
++ do j=1,3
++ incr(j)=d_t(j,i+1)-d_t(j,i)
++ enddo
++!c write (iout,*) i,(incr(j),j=1,3)
++!c write (iout,*) "Kinetic rotp:",i,(incr(j),j=1,3)
++ KEr_p=KEr_p+(incr(1)*incr(1)+incr(2)*incr(2)
++ & +incr(3)*incr(3))
++ enddo
++!c goto 111
++!c write(iout,*) 'KEr_p', KEr_p
++!c The rotational part of the side chain virtual bond
++ do i=innt,inct
++ iti=iabs(itype(i))
++ if (iti.ne.10) then
++ do j=1,3
++ incr(j)=d_t(j,nres+i)-d_t(j,i)
++ enddo
++!c write (iout,*) "Kinetic rotsc:",i,(incr(j),j=1,3)
++ KEr_sc=KEr_sc+Isc(iti)*(incr(1)*incr(1)+incr(2)*incr(2)+
++ & incr(3)*incr(3))
++ endif
++ enddo
++
++ enddo ! ichain
++!c The total kinetic energy
++ 111 continue
++!c write(iout,*) ' KEt_p',KEt_p,' KEt_sc',KEt_sc,' KEr_p',KEr_p,
++!c & ' KEr_sc', KEr_sc
++ KE_total=0.5d0*(mp*KEt_p+KEt_sc+0.25d0*Ip*KEr_p+KEr_sc)
++!c write (iout,*) "KE_total",KE_tota
++#else
++ write (iout,*) "Need to compile with -DFIVEDIAG to use this sub!"
++ stop
++#endif
++ return
++ end subroutine kinetic_CASC
++
! MD_A-MTS.F
!-----------------------------------------------------------------------------
subroutine MD
call hairpin(.true.,nharp,iharp)
call secondary2(.true.)
call pdbout(potE,tytul,ipdb)
++ call enerprint(potEcomp)
else
call cartout(totT)
endif
++ if (fodson) then
++ write(iout,*) "starting fodstep"
++ call fodstep(nfodstep)
++ write(iout,*) "after fodstep"
++ call statout(itime)
++ if(mdpdb) then
++ call hairpin(.true.,nharp,iharp)
++ call secondary2(.true.)
++ call pdbout(potE,tytul,ipdb)
++ else
++ call cartout(totT)
++ endif
++ endif
++
endif
if (rstcount.eq.1000.or.itime.eq.n_timestep) then
open(irest2,file=rest2name,status='unknown')
! Compute the acceleration due to friction forces (d_af_work) and stochastic
! forces (d_as_work)
!
++! call ginv_mult(fric_work, d_af_work)
++! call ginv_mult(stochforcvec, d_as_work)
++#ifdef FIVEDIAG
++ call fivediaginv_mult(dimen,fric_work, d_af_work)
++ call fivediaginv_mult(dimen,stochforcvec, d_as_work)
++#else
call ginv_mult(fric_work, d_af_work)
call ginv_mult(stochforcvec, d_as_work)
++#endif
++
return
end subroutine sddir_precalc
!-----------------------------------------------------------------------------
! Compute the acceleration due to friction forces (d_af_work) and stochastic
! forces (d_as_work)
!
++#ifdef FIVEDIAG
++ call fivediaginv_mult(maxres6,stochforcvec, d_as_work1)
++#else
call ginv_mult(stochforcvec, d_as_work1)
++#endif
!
! Update velocities
! include 'COMMON.NAMES'
! include 'COMMON.TIME1'
real(kind=8) :: xv,sigv,lowb,highb ,Ek1
++#ifdef FIVEDIAG
++ integer ichain,n,innt,inct,ibeg,ierr
++ double precision work(48*nres)
++ integer iwork(maxres6)
++ double precision Ghalf(mmaxres2_chain),Geigen(maxres2_chain),
++ & Gvec(maxres2_chain,maxres2_chain)
++ common /przechowalnia/Ghalf,Geigen,Gvec
++#ifdef DEBUG
++ double precision inertia(maxres2_chain,maxres2_chain)
++#endif
++#endif
!#define DEBUG
#ifdef FIVEDIAG
real(kind=8) ,allocatable, dimension(:) :: DDU1,DDU2,DL2,DL1,xsolv,DML,rs
M_PEP=0.0d0
do i=nnt,nct-1
mnum=molnum(i)
- if (mnum.eq.5) mp(mnum)=msc(itype(i,mnum),mnum)
- if (itype(i,mnum).eq.ntyp1_molec(mnum)) cycle
+ if (mnum.ge.5) mp(mnum)=msc(itype(i,mnum),mnum)
++ write(iout,*) "WTF",itype(i,mnum),i,mnum,mp(mnum)
+! if (itype(i,mnum).eq.ntyp1_molec(mnum)) cycle
M_PEP=M_PEP+mp(mnum)
+
do j=1,3
cm(j)=cm(j)+(c(j,i)+0.5d0*dc(j,i))*mp(mnum)
enddo
do j=1,3
cm(j)=cm(j)/(M_SC+M_PEP)
enddo
--
++! write(iout,*) "Center of mass:",cm
do i=nnt,nct-1
mnum=molnum(i)
- if (mnum.eq.5) mp(mnum)=msc(itype(i,mnum),mnum)
+ if (mnum.ge.5) mp(mnum)=msc(itype(i,mnum),mnum)
do j=1,3
pr(j)=c(j,i)+0.5d0*dc(j,i)-cm(j)
enddo
Im(2,2)=Im(2,2)+mp(mnum)*(pr(3)*pr(3)+pr(1)*pr(1))
Im(3,3)=Im(3,3)+mp(mnum)*(pr(1)*pr(1)+pr(2)*pr(2))
enddo
++
++! write(iout,*) "The angular momentum before msc add"
++! do i=1,3
++! write (iout,*) (Im(i,j),j=1,3)
++! enddo
do i=nnt,nct
mnum=molnum(i)
Im(2,2)=Im(2,2)+msc(iabs(iti),mnum)*(pr(3)*pr(3)+pr(1)*pr(1))
Im(3,3)=Im(3,3)+msc(iabs(iti),mnum)*(pr(1)*pr(1)+pr(2)*pr(2))
enddo
++! write(iout,*) "The angular momentum before Ip add"
++! do i=1,3
++! write (iout,*) (Im(i,j),j=1,3)
++! enddo
do i=nnt,nct-1
mnum=molnum(i)
Im(3,3)=Im(3,3)+Ip(mnum)*(1-dc_norm(3,i)*dc_norm(3,i))* &
vbld(i+1)*vbld(i+1)*0.25d0
enddo
++! write(iout,*) "The angular momentum before Isc add"
++! do i=1,3
++! write (iout,*) (Im(i,j),j=1,3)
++! enddo
do i=nnt,nct
endif
enddo
++! write(iout,*) "The angular momentum before agnom:"
++! do i=1,3
++! write (iout,*) (Im(i,j),j=1,3)
++! enddo
++
call angmom(cm,L)
! write(iout,*) "The angular momentum before adjustment:"
! write(iout,*) (L(j),j=1,3)
--
++! do i=1,3
++! write (iout,*) (Im(i,j),j=1,3)
++! enddo
Im(2,1)=Im(1,2)
Im(3,1)=Im(1,3)
Im(3,2)=Im(2,3)
! include 'COMMON.IOUNITS'
!el real(kind=8),dimension(6*nres) :: gamvec !(MAXRES6) maxres6=6*maxres
!el common /syfek/ gamvec
++#ifdef FIVEDIAG
++ integer iposc,ichain,n,innt,inct
++ double precision rs(nres+2)
++#endif
++
real(kind=8) :: vv(3),vvtot(3,nres),v_work(6*nres) !,&
!el ginvfric(2*nres,2*nres) !maxres2=2*maxres
!el common /przechowalnia/ ginvfric
checkmode=.false.
! if (large) lprn=.true.
! if (large) checkmode=.true.
++#ifdef FIVEDIAG
++c Here accelerations due to friction forces are computed right after forces.
++ d_t_work(:6*nres)=0.0d0
++ do j=1,3
++ v_work(j,1)=d_t(j,0)
++ v_work(j,nnt)=d_t(j,0)
++ enddo
++ do i=nnt+1,nct
++ do j=1,3
++ v_work(j,i)=v_work(j,i-1)+d_t(j,i-1)
++ enddo
++ enddo
++ do i=nnt,nct
++ mnum=molnum(i)
++ if (iabs(itype(i,1)).ne.10 .and. iabs(itype(i,mnum)).ne.ntyp1_molec(mnum).and.mnum.lt.3) then
++ do j=1,3
++ v_work(j,i+nres)=v_work(j,i)+d_t(j,i+nres)
++ enddo
++ endif
++ enddo
++#ifdef DEBUG
++ write (iout,*) "v_work"
++ do i=1,2*nres
++ write (iout,'(i5,3f10.5)') i,(v_work(j,i),j=1,3)
++ enddo
++#endif
++ do j=1,3
++ ind=0
++ do ichain=1,nchain
++ n=dimen_chain(ichain)
++ iposc=iposd_chain(ichain)
++c write (iout,*) "friction_force j",j," ichain",ichain,
++c & " n",n," iposc",iposc,iposc+n-1
++ innt=chain_border(1,ichain)
++ inct=chain_border(2,ichain)
++c diagnostics
++c innt=chain_border(1,1)
++c inct=chain_border(2,1)
++ do i=innt,inct
++ vvec(ind+1)=v_work(j,i)
++ ind=ind+1
++! if (iabs(itype(i)).ne.10) then
++ if (iabs(itype(i,1)).ne.10 .and. iabs(itype(i,mnum)).ne.ntyp1_molec(mnum).and.mnum.lt.3) then
++ vvec(ind+1)=v_work(j,i+nres)
++ ind=ind+1
++ endif
++ enddo
++#ifdef DEBUG
++ write (iout,*) "vvec ind",ind," n",n
++ write (iout,'(f10.5)') (vvec(i),i=iposc,ind)
++#endif
++c write (iout,*) "chain",i," ind",ind," n",n
++#ifdef TIMING
++#ifdef MPI
++ time01=MPI_Wtime()
++#else
++ time01=tcpu()
++#endif
++#endif
++ call fivediagmult(n,DMfric(iposc),DU1fric(iposc),
++ & DU2fric(iposc),vvec(iposc),rs)
++#ifdef TIMING
++#ifdef MPI
++ time_fricmatmult=time_fricmatmult+MPI_Wtime()-time01
++#else
++ time_fricmatmult=time_fricmatmult+tcpu()-time01
++#endif
++#endif
++#ifdef DEBUG
++ write (iout,*) "rs"
++ write (iout,'(f10.5)') (rs(i),i=1,n)
++#endif
++ do i=iposc,iposc+n-1
++c write (iout,*) "ichain",ichain," i",i," j",j,
++c & "index",3*(i-1)+j,"rs",rs(i-iposc+1)
++ fric_work(3*(i-1)+j)=-rs(i-iposc+1)
++ enddo
++ enddo
++ enddo
++#ifdef DEBUG
++ write (iout,*) "Vector fric_work dimen3",dimen3
++ write (iout,'(3f10.5)') (fric_work(j),j=1,dimen3)
++#endif
++#else
if(.not.allocated(gamvec)) allocate(gamvec(nres6)) !(MAXRES6)
if(.not.allocated(ginvfric)) allocate(ginvfric(nres2,nres2)) !maxres2=2*maxres
do i=0,nres2
enddo
enddo
endif
++#endif
return
end subroutine friction_force
!-----------------------------------------------------------------------------
real(kind=8) :: time00
logical :: lprn = .false.
integer :: i,j,ind,mnum
++#ifdef FIVEDIAG
++ integer ichain,innt,inct,iposc
++#endif
do i=0,2*nres
do j=1,3
#else
time_fsample=time_fsample+tcpu()-time00
#endif
++#ifdef FIVEDIAG
++ ind=0
++ do ichain=1,nchain
++ innt=chain_border(1,ichain)
++ inct=chain_border(2,ichain)
++ iposc=iposd_chain(ichain)
++!c for debugging only
++!c innt=chain_border(1,1)
++!c inct=chain_border(2,1)
++!c iposc=iposd_chain(1)
++!c write (iout,*)"stochastic_force ichain=",ichain," innt",innt,
++!c & " inct",inct," iposc",iposc
++ do j=1,3
++ stochforcvec(ind+j)=0.5d0*force(j,innt)
++ enddo
++ if (iabs(itype(innt),molnum(iint)).eq.10) then
++ do j=1,3
++ stochforcvec(ind+j)=stochforcvec(ind+j)+force(j,innt+nres)
++ enddo
++ ind=ind+3
++ else
++ ind=ind+3
++ do j=1,3
++ stochforcvec(ind+j)=force(j,innt+nres)
++ enddo
++ ind=ind+3
++ endif
++ do i=innt+1,inct-1
++ do j=1,3
++ stochforcvec(ind+j)=0.5d0*(force(j,i)+force(j,i-1))
++ enddo
++ if (iabs(itype(i,molnum(i)).eq.10) then
++ do j=1,3
++ stochforcvec(ind+j)=stochforcvec(ind+j)+force(j,i+nres)
++ enddo
++ ind=ind+3
++ else
++ ind=ind+3
++ do j=1,3
++ stochforcvec(ind+j)=force(j,i+nres)
++ enddo
++ ind=ind+3
++ endif
++ enddo
++ do j=1,3
++ stochforcvec(ind+j)=0.5d0*force(j,inct-1)
++ enddo
++ if (iabs(itype(inct),molnum(inct)).eq.10) then
++ do j=1,3
++ stochforcvec(ind+j)=stochforcvec(ind+j)+force(j,inct+nres)
++ enddo
++ ind=ind+3
++ else
++ ind=ind+3
++ do j=1,3
++ stochforcvec(ind+j)=force(j,inct+nres)
++ enddo
++ ind=ind+3
++ endif
++!c write (iout,*) "chain",ichain," ind",ind
++ enddo
++#ifdef DEBUG
++ write (iout,*) "stochforcvec"
++ write (iout,'(3f10.5)') (stochforcvec(j),j=1,ind)
++#endif
++#else
! Compute the stochastic forces acting on virtual-bond vectors.
do j=1,3
ff(j)=0.0d0
enddo
endif
--
++#endif
return
end subroutine stochastic_force
!-----------------------------------------------------------------------------
FC= ${INSTALL_DIR}/bin/mpif90
--OPT = -O3 -ip #-CA -CB
++OPT = -O3 -ip
#FFLAGS = -fpp -c ${OPT} -I$(INSTALL_DIR)/include
#-mcmodel large -check arg_temp_created -heap-arrays -recursive
.f90.o:
${FC} ${FFLAGS} ${CPPFLAGS} $*.f90
--DATA_FILE= ./data
--
--data = names.o io_units.o calc_data.o compare_data.o control_data.o \
++objects = xdrf/*.o names.o io_units.o calc_data.o compare_data.o control_data.o \
CSA_data.o energy_data.o geometry_data.o map_data.o \
-- MCM_data.o MD_data.o minim_data.o MPI_data.o REMD_data.o comm_local.o
--
--objects = xdrf/*.o \
++ MCM_data.o MD_data.o minim_data.o MPI_data.o REMD_data.o comm_local.o \
prng_32.o math.o random.o geometry.o md_calc.o io_base.o energy.o check_bond.o muca_md.o\
-- control.o io_config.o MPI.o minim.o fdisy.o fdiag.o machpd.o \
++ control.o io_config.o MPI.o minim.o \
regularize.o compare.o map.o REMD.o MCM_MD.o io.o \
-- MD.o MREMD.o CSA.o unres.o quindibisectok.o quindet2ok.o
++ MD.o MREMD.o CSA.o unres.o
#${EXE_FILE}: ${objects}
#NOMPI: EXE_FILE = ../../bin/unres_MD-M_NO_MPI_F90_EL.exe
NOMPI: EXE_FILE = ../../bin/unres_NO_MPI_F90_EL.exe
--NOMPI: ${data} ${objects}
++NOMPI: ${objects}
cc -o compinfo compinfo.c
./compinfo | true
${FC} ${FFLAGS} cinfo.f90
-- ${FC} ${data} ${objects} cinfo.o -o ${EXE_FILE}
++ ${FC} ${objects} cinfo.o -o ${EXE_FILE}
# ${FC} ${objects} -Xlinker -M -o ${EXE_FILE}
GAB: CPPFLAGS = -DPROCOR -DLINUX -DPGI -DAMD64 -DUNRES -DISNAN -DMP -DMPI \
-DSPLITELE -DLANG0 -DCRYST_BOND -DCRYST_THETA -DCRYST_SC
#GAB: EXE_FILE = ../../bin/unres_MD-M_GAB_F90_EL_opt3.exe
GAB: EXE_FILE = ../../bin/unres_GAB_F90_EL.exe
--GAB: ${data} ${objects}
++GAB: ${objects}
cc -o compinfo compinfo.c
./compinfo | true
${FC} ${FFLAGS} cinfo.f90
-- ${FC} ${OPT} ${data} ${objects} cinfo.o -o ${EXE_FILE}
++ ${FC} ${OPT} ${objects} cinfo.o -o ${EXE_FILE}
4P: CPPFLAGS = -DLINUX -DPGI -DAMD64 -DUNRES -DISNAN -DMP -DMPI \
-DSPLITELE -DLANG0 -DCRYST_BOND -DCRYST_THETA -DCRYST_SC
#4P: EXE_FILE = ../../bin/unres_MD-M_4P_F90_EL_opt3.exe
4P: EXE_FILE = ../../bin/unres_4P_F90_EL.exe
--4P: ${data}${objects}
++4P: ${objects}
cc -o compinfo compinfo.c
./compinfo | true
${FC} ${FFLAGS} cinfo.f90
-- ${FC} ${OPT} ${data} ${objects} cinfo.o -o ${EXE_FILE}
++ ${FC} ${OPT} ${objects} cinfo.o -o ${EXE_FILE}
E0LL2Y: CPPFLAGS = -DPROCOR -DLINUX -DPGI -DAMD64 -DUNRES -DISNAN -DMP -DMPI \
-- -DSPLITELE -DLANG0 -DFIVEDIAG
--#E0LL2Y: EXE_FILE = ../../bin/unres_E0LL2Y_F90_EL.exe
--E0LL2Y: EXE_FILE = ../../bin/unres_E0LL2Y_5DiaF90_EL.exe
--#E0LL2Y: EXE_FILE = ../../bin/unres_E0LL2Y_5DiaF90_ELcb.exe
--#E0LL2Y: EXE_FILE = ../../bin/unres_E0LL2Y_5DiaF90_EL.diag.exe
--E0LL2Y: ${data} ${objects}
-- cc -o compinfo compinfo.c
-- ./compinfo | true
-- ${FC} ${FFLAGS} cinfo.f90
-- ${FC} ${OPT} ${data} ${objects} cinfo.o -o ${EXE_FILE}
--
--NEWGRAD: CPPFLAGS = -DPROCOR -DLINUX -DPGI -DAMD64 -DUNRES -DISNAN -DMP -DMPI \
-- -DSPLITELE -DLANG0 -DCARGRAD -DFIVEDIAG
--NEWGRAD: EXE_FILE = ../../bin/unres_E0LL2Y_F90_EL-NEWG.exe
--NEWGRAD: ${data} ${objects}
++ -DSPLITELE -DLANG0
++#E0LL2Y: EXE_FILE = ../../bin/unres_MD-M_E0LL2Y_F90_EL_opt3.exe
++E0LL2Y: EXE_FILE = ../../bin/unres_E0LL2Y_F90_EL.exe
++E0LL2Y: ${objects}
cc -o compinfo compinfo.c
./compinfo | true
${FC} ${FFLAGS} cinfo.f90
-- ${FC} ${OPT} ${data} ${objects} cinfo.o -o ${EXE_FILE}
++ ${FC} ${OPT} ${objects} cinfo.o -o ${EXE_FILE}
xdrf/*.o:
cd xdrf && make
clean:
-- rm -f *.o && rm -f *.mod && rm -f compinfo && cd xdrf && make clean
--# rm -f *.o && rm -f *.mod && rm ${EXE_FILE} && rm -f compinfo && cd xdrf && make clean
++ rm -f *.o && rm -f *.mod && rm ${EXE_FILE} && rm -f compinfo && cd xdrf && make clean
--names.o: ${DATA_FILE}/names.f90
-- ${FC} ${FFLAGS} ${CPPFLAGS} ${DATA_FILE}/names.f90
++names.o: names.f90
++ ${FC} ${FFLAGS} ${CPPFLAGS} names.f90
--io_units.o: ${DATA_FILE}/io_units.f90
-- ${FC} ${FFLAGS} ${CPPFLAGS} ${DATA_FILE}/io_units.f90
++io_units.o: io_units.f90
++ ${FC} ${FFLAGS} ${CPPFLAGS} io_units.f90
--calc_data.o: ${DATA_FILE}/calc_data.f90
-- ${FC} ${FFLAGS} ${CPPFLAGS} ${DATA_FILE}/calc_data.f90
++calc_data.o: calc_data.f90
++ ${FC} ${FFLAGS} ${CPPFLAGS} calc_data.f90
--compare_data.o: ${DATA_FILE}/compare_data.f90
-- ${FC} ${FFLAGS} ${CPPFLAGS} ${DATA_FILE}/compare_data.f90
++compare_data.o: compare_data.f90
++ ${FC} ${FFLAGS} ${CPPFLAGS} compare_data.f90
--control_data.o: ${DATA_FILE}/control_data.f90
-- ${FC} ${FFLAGS} ${CPPFLAGS} ${DATA_FILE}/control_data.f90
++control_data.o: control_data.f90
++ ${FC} ${FFLAGS} ${CPPFLAGS} control_data.f90
--CSA_data.o: ${DATA_FILE}/CSA_data.f90
-- ${FC} ${FFLAGS} ${CPPFLAGS} ${DATA_FILE}/CSA_data.f90
++CSA_data.o: CSA_data.f90
++ ${FC} ${FFLAGS} ${CPPFLAGS} CSA_data.f90
--energy_data.o: ${DATA_FILE}/energy_data.f90
-- ${FC} ${FFLAGS} ${CPPFLAGS} ${DATA_FILE}/energy_data.f90
++energy_data.o: energy_data.f90
++ ${FC} ${FFLAGS} ${CPPFLAGS} energy_data.f90
--geometry_data.o: ${DATA_FILE}/geometry_data.f90
-- ${FC} ${FFLAGS} ${CPPFLAGS} ${DATA_FILE}/geometry_data.f90
++geometry_data.o: geometry_data.f90
++ ${FC} ${FFLAGS} ${CPPFLAGS} geometry_data.f90
--map_data.o: ${DATA_FILE}/map_data.f90
-- ${FC} ${FFLAGS} ${CPPFLAGS} ${DATA_FILE}/map_data.f90
++map_data.o: map_data.f90
++ ${FC} ${FFLAGS} ${CPPFLAGS} map_data.f90
--MCM_data.o: ${DATA_FILE}/MCM_data.f90
-- ${FC} ${FFLAGS} ${CPPFLAGS} ${DATA_FILE}/MCM_data.f90
++MCM_data.o: MCM_data.f90
++ ${FC} ${FFLAGS} ${CPPFLAGS} MCM_data.f90
--MD_data.o: ${DATA_FILE}/MD_data.f90
-- ${FC} ${FFLAGS} ${CPPFLAGS} ${DATA_FILE}/MD_data.f90
++MD_data.o: MD_data.f90
++ ${FC} ${FFLAGS} ${CPPFLAGS} MD_data.f90
--minim_data.o: ${DATA_FILE}/minim_data.f90
-- ${FC} ${FFLAGSm} ${CPPFLAGS} ${DATA_FILE}/minim_data.f90
++minim_data.o: minim_data.f90
++ ${FC} ${FFLAGSm} ${CPPFLAGS} minim_data.f90
--MPI_data.o: ${DATA_FILE}/MPI_data.f90
-- ${FC} ${FFLAGS} ${CPPFLAGS} ${DATA_FILE}/MPI_data.f90
++MPI_data.o: MPI_data.f90
++ ${FC} ${FFLAGS} ${CPPFLAGS} MPI_data.f90
--REMD_data.o: ${DATA_FILE}/REMD_data.f90
-- ${FC} ${FFLAGS} ${CPPFLAGS} ${DATA_FILE}/REMD_data.f90
++REMD_data.o: REMD_data.f90
++ ${FC} ${FFLAGS} ${CPPFLAGS} REMD_data.f90
--comm_local.o: ${DATA_FILE}/comm_local.f90
-- ${FC} ${FFLAGS} ${CPPFLAGS} ${DATA_FILE}/comm_local.f90
++comm_local.o: comm_local.f90
++ ${FC} ${FFLAGS} ${CPPFLAGS} comm_local.f90
prng_32.o: prng_32.f90
${FC} ${FFLAGS} ${CPPFLAGS} prng_32.f90
check_bond.o: check_bond.f90
${FC} ${FFLAGS} ${CPPFLAGS} check_bond.f90
--control.o: control.F90
-- ${FC} ${FFLAGS} ${CPPFLAGS} control.F90
++control.o: control.f90
++ ${FC} ${FFLAGS} ${CPPFLAGS} control.f90
io_config.o: io_config.f90
${FC} ${FFLAGS2} ${CPPFLAGS} io_config.f90
regularize.o: regularize.f90
${FC} ${FFLAGS} ${CPPFLAGS} regularize.f90
--compare.o: compare.F90
-- ${FC} ${FFLAGS} ${CPPFLAGS} compare.F90
++compare.o: compare.f90
++ ${FC} ${FFLAGS} ${CPPFLAGS} compare.f90
map.o: map.f90
${FC} ${FFLAGS} ${CPPFLAGS} map.f90
unres.o: unres.f90
${FC} ${FFLAGS} ${CPPFLAGS} unres.f90
--
--quindibisectok.o: quindibisectok.F90
-- ${FC} ${FFLAGS} ${CPPFLAGS} quindibisectok.F90
--
--quindet2ok.o: quindet2ok.F90
-- ${FC} ${FFLAGS} ${CPPFLAGS} quindet2ok.F90
--
--
--
--
--
--
--
--
--
! IONS
iion=401
iionnucl=402
+ iiontran=403 ! this is parameter file for transition metals
++ iwaterwater=404
++ iwatersc=405
#if defined(WHAM_RUN) || defined(CLUSTER)
!
! setting the mpi variables for WHAM
!
!c maxfun=5000
!c maxit=2000
-- maxfun=500
-- maxit=200
++ maxfun=1000
++ maxit=1000
tolf=1.0D-2
rtolf=5.0D-4
!
call int_bounds &
(ntheta_constr,ithetaconstr_start,ithetaconstr_end)
endif
+! HERE MAKING LISTS FOR MARTINI
+ itmp=0
+ do i=1,3
+ itmp=itmp+nres_molec(i)
+ enddo
+!First bonding
+! call int_bounds(nres_molec(4)-1,ilipbond_start,ilipbond_end)
+ ilipbond_start=1+itmp
+ ilipbond_end=nres_molec(4)-1+itmp
+!angles
++ call int_bounds(nres_molec(4)-1,ilipbond_start_tub,ilipbond_end_tub)
++ ilipbond_start_tub=1+itmp
++ ilipbond_end_tub=nres_molec(4)-1+itmp
+
+! call int_bounds(nres_molec(4)-2,ilipang_start,ilipang_end)
+ ilipang_start=2+itmp
+ ilipang_end=itmp+nres_molec(4)-1
+! create LJ LIST MAXIMUM
+! Eliminate branching from list
+ remmat=0
+ do i=1+itmp,nres_molec(4)-1+itmp
+ if (itype(i,4).eq.12) ibra=i
+ if (itype(i,4).eq.ntyp1_molec(4)-1) then
+! remmat(ibra-1,i+1)=1
+ remmat(ibra,i+1)=1
+! remmat(ibra+1,i+1)=1
+ endif
+ enddo
+ maxljliplist=0
++ if (.not.allocated(mlipljlisti)) then
+ allocate (mlipljlisti(nres_molec(4)*nres_molec(4)/2))
+ allocate (mlipljlistj(nres_molec(4)*nres_molec(4)/2))
++ endif
+ do i=1+itmp,nres_molec(4)-1+itmp
+ do j=i+2,nres_molec(4)+itmp
+ if ((itype(i,4).le.ntyp_molec(4)).and.(itype(j,4).le.ntyp_molec(4))&
+ .and.(remmat(i,j).eq.0)) then
+ maxljliplist=maxljliplist+1
+ mlipljlisti(maxljliplist)=i
+ mlipljlistj(maxljliplist)=j
+ if (energy_dec) print *,i,j,remmat(i,j),"lj lip list"
+ endif
+ enddo
+ enddo
+! split the bound of the list
+ call int_bounds(maxljliplist,iliplj_start,iliplj_end)
+ iliplj_start=iliplj_start
+ iliplj_end=iliplj_end
+! now the electrostatic list
+ maxelecliplist=0
++ if (.not.allocated(mlipeleclisti)) then
+ allocate (mlipeleclisti(nres_molec(4)*nres_molec(4)/2))
+ allocate (mlipeleclistj(nres_molec(4)*nres_molec(4)/2))
++ endif
+ do i=1+itmp,nres_molec(4)-1+itmp
+ do j=i+2,nres_molec(4)+itmp
+ if ((itype(i,4).le.4).and.(itype(j,4).le.4)) then
+ maxelecliplist=maxelecliplist+1
+ mlipeleclisti(maxelecliplist)=i
+ mlipeleclistj(maxelecliplist)=j
+ endif
+ enddo
+ enddo
+ call int_bounds(maxelecliplist,ilip_elec_start,ilipelec_end)
+ ilip_elec_start=ilip_elec_start
+ ilipelec_end=ilipelec_end
! nsumgrad=(nres-nnt)*(nres-nnt+1)/2
! nlen=nres-nnt+1
nsumgrad=(nres-nnt)*(nres-nnt+1)/2
real(kind=8) :: v_ini,d_time,d_time0,scal_fric,&
t_bath,tau_bath,dvmax,damax
integer :: n_timestep,ntime_split,ntime_split0,maxtime_split,&
-- ntwx,ntwe
-- logical :: mdpdb,large,print_compon,tbf,rest
++ ntwx,ntwe,nfodstep
++ logical :: mdpdb,large,print_compon,tbf,rest,fodson
! common /MDcalc/
real(kind=8) :: totT,totE,potE,EK,amax,edriftmax,kinetic_T,totTafm
real(kind=8),dimension(:),allocatable :: potEcomp !(0:n_ene+4)
short_r_sidechain
real(kind=8) :: VSolvSphere,VSolvSphere_div,buff_shield
! AFM
-- real(kind=8) :: distafminit,forceAFMconst,velAFMconst
-- integer :: afmend,afmbeg
++ real(kind=8) :: distafminit,forceAFMconst,velAFMconst,&
++ velnanoconst,distnanoinit,forcenanoconst,inanomove,vecsim,vectrue
++ real(kind=8),dimension(1000) :: inanotab
++ integer :: afmend,afmbeg,nbegafmmat,nendafmmat
++ integer, dimension(1000) :: afmendcentr,afmbegcentr
real(kind=8),dimension(:,:), allocatable :: catprm
real(kind=8),dimension(:,:,:), allocatable :: catnuclprm
!end of ions parameters by Agnieszka Lipska (Ca, K, Na, Mg, Cl)-----------------------
!
+
+! Parameters for transistion ions
+ real(kind=8),dimension(:,:,:),allocatable:: agamacattran,&
+ athetacattran
+ real(kind=8),dimension(:,:),allocatable::acatshiftdsc,&
+ bcatshiftdsc,demorsecat,alphamorsecat,x0catleft,x0catright,&
+ x0cattrans,aomicattr
+ real(kind=8),dimension(:),allocatable::ntrantyp
+
! FRAGMENT FOR INTERACTION LIST
integer,dimension(:),allocatable :: newcontlistppi,newcontlistppj,&
- newcontlisti,newcontlistj, newcontlistscpi,newcontlistscpj
+ newcontlisti,newcontlistj, newcontlistscpi,newcontlistscpj,&
+ newcontlistcatscnormi,newcontlistcatscnormj,&
+ newcontlistcatpnormi,newcontlistcatpnormj,&
+ newcontlistcatsctrani,newcontlistcatsctranj,&
+ newcontlistcatptrani,newcontlistcatptranj,&
+ newcontlistcatscangi,newcontlistcatscangj,&
+ newcontlistcatscangfi,newcontlistcatscangfj,&
+ newcontlistcatscangfk,&
+ newcontlistcatscangti,newcontlistcatscangtj,&
+ newcontlistcatscangtk,newcontlistcatscangtl
+
+
+
+
integer :: g_listpp_start,g_listpp_end,g_listscp_start,g_listscp_end,&
- g_listscsc_start,g_listscsc_end
+ g_listscsc_start,g_listscsc_end, &
+ g_listcatsctran_start,g_listcatsctran_end,&
+ g_listcatscnorm_start,g_listcatscnorm_end,&
+ g_listcatptran_start,g_listcatptran_end,&
+ g_listcatpnorm_start,g_listcatpnorm_end,&
+ g_ilist_catscnorm,g_ilist_catsctran,g_ilist_catpnorm,&
+ g_ilist_catptran,g_ilist_catscang,g_ilist_catscangf,g_ilist_catscangt,&
+ g_listcatscang_start,g_listcatscang_end,&
+ g_listcatscangf_start,g_listcatscangf_end,&
+ g_listcatscangt_start,g_listcatscangt_end
+
+
+! MARTINI FORCE FIELD
+ integer :: ilipbond_start,ilipbond_end,ilipang_start,ilipang_end, &
- maxelecliplist,ilip_elec_start,ilipelec_end,maxljliplist,iliplj_start,iliplj_end
++ maxelecliplist,ilip_elec_start,ilipelec_end,maxljliplist,iliplj_start,iliplj_end,&
++ ilipbond_start_tub,ilipbond_end_tub
+ integer,dimension(:),allocatable :: mlipljlisti,mlipljlistj,&
+ mlipeleclisti,mlipeleclistj
+ real(kind=8),dimension(:,:,:),allocatable :: lip_angle_force,lip_angle_angle
+ real(kind=8),dimension(:,:),allocatable :: lip_bond,lip_eps,lip_sig
+ integer,dimension(:),allocatable :: ichargelipid
+ real(kind=8) :: kjtokcal,krad,k_coulomb_lip,kbondlip
+ !homology
+ integer :: inprint,npermut,&
+ tubelog,constr_homology,homol_nset
+ logical :: mremd_dec,out_cart,&
+ out_int,gmatout,&
+ with_dihed_constr,read2sigma,start_from_model,read_homol_frag,&
+ out_template_coord,out_template_restr,loc_qlike,adaptive
+ real(kind=8) :: aincr,waga_dist,waga_angle,waga_theta,&
+ waga_d,dist2_cut
+ real(kind=8),dimension(:),allocatable :: waga_homology
+ real(kind=8),dimension(:,:),allocatable :: odl,&
+ sigma_odl,dih,sigma_dih, sigma_odlir, xxtpl,&
+ yytpl,zztpl,thetatpl,sigma_theta,sigma_d
+ integer,dimension(:),allocatable :: ires_homo,jres_homo
+ integer,dimension(:,:),allocatable :: idomain,tabpermchain,iequiv,&
+ chain_border,chain_border1
+ integer :: lim_odl,lim_dih,link_start_homo,&
+ link_end_homo,idihconstr_start_homo,idihconstr_end_homo
+ logical,dimension(:,:),allocatable :: l_homo
+ integer ::nchain,iprzes,&
+ npermchain,&
+ nchain_group,&
+ nmodel_start,nran_start
+ ! real(kind=8),dimension(:,:),allocatable :: c,dc,dc_old,xloc,xrot,&
+ ! dc_norm,dc_norm2,cref,crefjlee
+ ! real(kind=8),dimension(:),allocatable :: d_c_work
+ real(kind=8),dimension(:,:,:),allocatable :: chomo
+ ! real(kind=8) :: totTafm
+ character(len=256),dimension(:),allocatable:: pdbfiles_chomo
+ integer,dimension(:),allocatable :: chain_length,ireschain,&
+ nequiv,mapchain, nres_chomo
+ real(kind=8) :: enecut,sscut,sss,sssgrad
++! waterwater
++ real(kind=8),dimension(:),allocatable :: awaterenta,bwaterenta,&
++ cwaterenta,dwaterenta,awaterentro,bwaterentro,cwaterentro,&
++ dwaterentro
+ ! buflipbot, bufliptop,bordlipbot,bordliptop,lipbufthick,lipthick
++!-------------------------------------------------------------------------
++ real(kind=8),dimension(3,70000) :: ea
+ ! real(kind=8) :: buftubebot, buftubetop,bordtubebot,bordtubetop,tubebufthick
end module energy_data
ithep_pdb,irotam_pdb,iliptranpar,itube, &
ibond_nucl,ithep_nucl,irotam_nucl,itorp_nucl,itordp_nucl, &
isidep_nucl,iscpp_nucl,isidep_scbase,isidep_pepbase,isidep_scpho,&
- isidep_peppho,iion,iionnucl,iiontran,ilipbond,ilipnonbond
- isidep_peppho,iion,iionnucl
++ isidep_peppho,iion,iionnucl,iiontran,ilipbond,ilipnonbond,&
++ iwaterwater,iwatersc
#ifdef WHAM_RUN
! el wham iounits
integer :: isidep1,ihist,iweight,izsc,idistr
bondname_nucl,thetname_nucl,rotname_nucl,torname_nucl, &
tordname_nucl,sidename_nucl,scpname_nucl, &
sidename_scbase,pepname_pepbase,pepname_scpho,pepname_peppho, &
- ionname,ionnuclname,iontranname,lipbondname,lipnonbondname
- ionname,ionnuclname
++ ionname,ionnuclname,iontranname,lipbondname,lipnonbondname,&
++ iwaterwatername,iwaterscname
!-----------------------------------------------------------------------
! INP - main input file
! IOUT - list file
' ',' ',' ',' ',' ',' ',' ',' ',' ',' ', &
' ',' ',' ',&
' ',' ',' ',' ',' ',' ',' ',' ',' ',' ',&
-- ' ',' ',' ',' ',' ',' ',&
- 'NA+','MG2','K+ ','CA2','CL-',' ',' ',' ',&
++ ' ',' ',' ',' ','WAT',' ',&
+ 'NA+','MG2','K+ ','CA2','CL-','ZN2',' ',' ',&
' ',' ',' ',' ',' ',' ',' ',' ',' ',' ',&
' ',' ',' ',' ',' ',' ',' ',' ',' ',' '&
/))
"WTORD_NUCL","WCORR_NUCL","WCORR3_NUC","WNULL ","WNULL ",&
"WCATPROT ","WCATCAT ","WNULL ","WNULL ","WNULL ",&
"WSCBASE ","WPEPBASE ","WSCPHO ","WPEPPHO ","WCATNUCL ",&
- "WNULL ","WNULL ","WNULL ","WNULL ","WNULL ",&
- "H_CONS"/)
++ "H_CONS ","WNULL ","WNULL ","WNULL ","WNULL ",&
+ "WCATTRAN ","WCATANG "/)
integer :: nprint_ene = 21
integer,dimension(n_ene) :: print_order = &
! common /przechowalnia/
real(kind=8),dimension(:,:,:),allocatable :: zapas
real(kind=8),dimension(:,:,:,:),allocatable ::zapas2 !(max_dim,maxconts,max_fg_procs)
++#ifdef FIVEDIAG
++ real(kind=8),dimension(:,:),allocatable :: fromto !(3,3,maxdim)(maxdim=(maxres-1)*(maxres-2)/2)
++#else
real(kind=8),dimension(:,:,:),allocatable :: fromto !(3,3,maxdim)(maxdim=(maxres-1)*(maxres-2)/2)
++#endif
!-----------------------------------------------------------------------------
!-----------------------------------------------------------------------------
!
call escp_soft_sphere(evdw2,evdw2_14)
endif
! write(iout,*) "in etotal before ebond",ipot
--
++! print *,"after escp"
!
! Calculate the bond-stretching energy
!
! Calculate the disulfide-bridge and other energy and the contributions
! from other distance constraints.
! print *,'Calling EHPB'
-- call edis(ehpb)
++! call edis(ehpb)
!elwrite(iout,*) "in etotal afer edis",ipot
! print *,'EHPB exitted succesfully.'
!
ebe=0.0d0
endif
ethetacnstr=0.0d0
++! write(iout,*) with_theta_constr,"with_theta_constr"
if (with_theta_constr) call etheta_constr(ethetacnstr)
! write(iout,*) "in etotal afer ebe",ipot
! Calculate the SC local energy.
!
call esc(escloc)
--!elwrite(iout,*) "in etotal afer esc",ipot
++! print *, "in etotal afer esc",wtor
! print *,"Processor",myrank," computed USC"
!
! Calculate the virtual-bond torsional energy.
! edihcnstr=0
! endif
if (wtor.gt.0.0d0) then
++! print *,"WTOR",wtor,tor_mode
if (tor_mode.eq.0) then
call etor(etors)
else
if (ndih_constr.gt.0) call etor_constr(edihcnstr)
!c print *,"Processor",myrank," computed Utor"
++! print *, "constr_homol",constr_homology
! print *,"Processor",myrank," computed Utor"
-
+ if (constr_homology.ge.1) then
+ call e_modeller(ehomology_constr)
+ ! print *,'iset=',iset,'me=',me,ehomology_constr,
+ ! & 'Processor',fg_rank,' CG group',kolor,
+ ! & ' absolute rank',MyRank
+ ! print *,"tu"
+ else
+ ehomology_constr=0.0d0
+ endif
+
!
! 6/23/01 Calculate double-torsional energy
!
--!elwrite(iout,*) "in etotal",ipot
++! print *, "before etor_d",wtor_d
if (wtor_d.gt.0) then
call etor_d(etors_d)
else
else
eliptran=0.0d0
endif
+ else
+ eliptran=0.0d0
+ evdw=0.0d0
+#ifdef SCP14
+ evdw2=0.0d0
+ evdw2_14=0.0d0
+#else
+ evdw2=0.0d0
+#endif
+#ifdef SPLITELE
+ ees=0.0d0
+ evdw1=0.0d0
+#else
+ ees=0.0d0
+ evdw1=0.0d0
+#endif
+ ecorr=0.0d0
+ ecorr5=0.0d0
+ ecorr6=0.0d0
+ eel_loc=0.0d0
+ eello_turn3=0.0d0
+ eello_turn4=0.0d0
+ eturn6=0.0d0
+ ebe=0.0d0
+ escloc=0.0d0
+ etors=0.0d0
+ etors_d=0.0d0
+ ehpb=0.0d0
+ edihcnstr=0.0d0
+ estr=0.0d0
+ Uconst=0.0d0
+ esccor=0.0d0
-
++ ehomology_constr=0.0d0
++ ethetacnstr=0.0d0
+ endif !nres_molec(1)
++! write(iout,*) "TU JEST PRZED EHPB"
++! call edis(ehpb)
if (fg_rank.eq.0) then
if (AFMlog.gt.0) then
call AFMforce(Eafmforce)
Eafmforce=0.0d0
endif
endif
++! print *,"before tubemode",tubemode
if (tubemode.eq.1) then
call calctube(etube)
else if (tubemode.eq.2) then
else
etube=0.0d0
endif
++! print *, "TU JEST PRZED EHPB"
++ call edis(ehpb)
++
!--------------------------------------------------------
--! write (iout,*) "NRES_MOLEC(2),",nres_molec(2)
++! print *, "NRES_MOLEC(2),",nres_molec(2)
! print *,"before",ees,evdw1,ecorr
! write(iout,*) ecorr_nucl,"ecorr_nucl",nres_molec(2)
if (nres_molec(2).gt.0) then
! write(iout,*) ecorr_nucl,"ecorr_nucl",nres_molec(2)
! print *,"before ecatcat",wcatcat
if (nres_molec(5).gt.0) then
- if (g_ilist_catsctran.gt.0) then
- if (nfgtasks.gt.1) then
- if (fg_rank.eq.0) then
- call ecatcat(ecationcation)
- endif
- else
- call ecatcat(ecationcation)
- endif
- if (oldion.gt.0) then
- call ecat_prot(ecation_prot)
- else
- call ecats_prot_amber(ecation_prot)
- endif
++ if (g_ilist_catsctran.gt.0) then
+ call ecat_prot_transition(ecat_prottran)
- else
- ecat_prottran=0.0d0
- endif
- if (g_ilist_catscang.gt.0) then
++ else
++ ecat_prottran=0.0d0
++ endif
++ if (g_ilist_catscang.gt.0) then
+ call ecat_prot_ang(ecation_protang)
- else
- ecation_protang=0.0d0
- endif
- if (nfgtasks.gt.1) then
- if (fg_rank.eq.0) then
- if (nres_molec(5).gt.1) call ecatcat(ecationcation)
- endif
- else
++ else
++ ecation_protang=0.0d0
++ endif
++ if (nfgtasks.gt.1) then
++ if (fg_rank.eq.0) then
++ if (nres_molec(5).gt.1) call ecatcat(ecationcation)
++ endif
++ else
+ if (nres_molec(5).gt.1) call ecatcat(ecationcation)
- endif
- if (oldion.gt.0) then
- if (g_ilist_catpnorm.gt.0) call ecat_prot(ecation_prot)
- else
- if (g_ilist_catpnorm.gt.0) call ecats_prot_amber(ecation_prot)
- endif
++ endif
++ if (oldion.gt.0) then
++ if (g_ilist_catpnorm.gt.0) call ecat_prot(ecation_prot)
++ else
++ if (g_ilist_catpnorm.gt.0) call ecats_prot_amber(ecation_prot)
++ endif
else
ecationcation=0.0d0
ecation_prot=0.0d0
++ ecation_protang=0.0d0
++ ecat_prottran=0.0d0
endif
+ if (g_ilist_catscnorm.eq.0) ecation_prot=0.0d0
if ((nres_molec(2).gt.0).and.(nres_molec(1).gt.0)) then
call eprot_sc_base(escbase)
call epep_sc_base(epepbase)
energia(49)=epeppho
! energia(50)=ecations_prot_amber
energia(50)=ecation_nucl
+ energia(51)=ehomology_constr
+! energia(51)=homology
+ energia(52)=elipbond
+ energia(53)=elipang
+ energia(54)=eliplj
+ energia(55)=elipelec
+ energia(56)=ecat_prottran
+ energia(57)=ecation_protang
+! write(iout,*) elipelec,"elipelec"
+! write(iout,*) elipang,"elipang"
+! write(iout,*) eliplj,"eliplj"
call sum_energy(energia,.true.)
if (dyn_ss) call dyn_set_nss
! print *," Processor",myrank," left SUM_ENERGY"
eliptran,etube, Eafmforce,ethetacnstr
real(kind=8) :: evdwpp,eespp,evdwpsb,eelpsb,evdwsb,eelsb,estr_nucl,&
ebe_nucl,esbloc,etors_nucl,etors_d_nucl,ecorr_nucl,&
- ecorr3_nucl
+ ecorr3_nucl,ehomology_constr
real(kind=8) :: ecation_prot,ecationcation,ecations_prot_amber,&
- ecation_nucl
+ ecation_nucl,ecat_prottran,ecation_protang
real(kind=8) :: escbase,epepbase,escpho,epeppho
integer :: i
+ real(kind=8) :: elipbond,elipang,eliplj,elipelec
#ifdef MPI
integer :: ierr
real(kind=8) :: time00
escpho=energia(48)
epeppho=energia(49)
ecation_nucl=energia(50)
+ ehomology_constr=energia(51)
+ elipbond=energia(52)
+ elipang=energia(53)
+ eliplj=energia(54)
+ elipelec=energia(55)
+ ecat_prottran=energia(56)
+ ecation_protang=energia(57)
! ecations_prot_amber=energia(50)
! energia(41)=ecation_prot
+wtor_d_nucl*etors_d_nucl+wcorr_nucl*ecorr_nucl+wcorr3_nucl*ecorr3_nucl&
+wcatprot*ecation_prot+wcatcat*ecationcation+wscbase*escbase&
+wpepbase*epepbase+wscpho*escpho+wpeppho*epeppho+wcatnucl*ecation_nucl&
- +elipbond+elipang+eliplj+elipelec+wcat_tran*ecat_prottran+ecation_protang
++ +elipbond+elipang+eliplj+elipelec+wcat_tran*ecat_prottran+ecation_protang&
+ #ifdef WHAM_RUN
+ +0.0d0
+ #else
+ +ehomology_constr
+ #endif
#else
etot=wsc*evdw+wscp*evdw2+welec*(ees+evdw1) &
+wang*ebe+wtor*etors+wscloc*escloc &
+wvdwsb*evdwsb+welsb*eelsb+wsbloc*esbloc+wtor_nucl*etors_nucl&
+wtor_d_nucl*etors_d_nucl+wcorr_nucl*ecorr_nucl+wcorr3_nucl*ecorr3_nucl&
+wcatprot*ecation_prot+wcatcat*ecationcation+wscbase*escbase&
- +wpepbase*epepbase+wscpho*escpho+wpeppho*epeppho+wcatnucl*ecation_nucl
+ +wpepbase*epepbase+wscpho*escpho+wpeppho*epeppho+wcatnucl*ecation_nucl&
- +elipbond+elipang+eliplj+elipelec+wcat_tran*ecat_prottran+ecation_protang
++ +elipbond+elipang+eliplj+elipelec+wcat_tran*ecat_prottran+ecation_protang&
+ #ifdef WHAM_RUN
+ +0.0d0
+ #else
+ +ehomology_constr
+ #endif
#endif
energia(0)=etot
! detecting NaNQ
etube,ethetacnstr,Eafmforce
real(kind=8) :: evdwpp,eespp,evdwpsb,eelpsb,evdwsb,eelsb,estr_nucl,&
ebe_nucl,esbloc,etors_nucl,etors_d_nucl,ecorr_nucl,&
- ecorr3_nucl
+ ecorr3_nucl,ehomology_constr
real(kind=8) :: ecation_prot,ecationcation,ecations_prot_amber,&
- ecation_nucl
+ ecation_nucl,ecat_prottran,ecation_protang
real(kind=8) :: escbase,epepbase,escpho,epeppho
-
+ real(kind=8) :: elipbond,elipang,eliplj,elipelec
etot=energia(0)
evdw=energia(1)
evdw2=energia(2)
escpho=energia(48)
epeppho=energia(49)
ecation_nucl=energia(50)
+ elipbond=energia(52)
+ elipang=energia(53)
+ eliplj=energia(54)
+ elipelec=energia(55)
+ ecat_prottran=energia(56)
+ ecation_protang=energia(57)
+ ehomology_constr=energia(51)
+
! ecations_prot_amber=energia(50)
#ifdef SPLITELE
write (iout,10) evdw,wsc,evdw2,wscp,ees,welec,evdw1,wvdwpp,&
evdwpp,wvdwpp_nucl,eespp,welpp,evdwpsb,wvdwpsb,eelpsb,welpsb,&
evdwsb,wvdwsb,eelsb,welsb,esbloc,wsbloc,etors_nucl,wtor_nucl,&
etors_d_nucl,wtor_d_nucl,ecorr_nucl,wcorr_nucl,&
- ecorr3_nucl,wcorr3_nucl,ecation_prot,wcatprot,ecationcation,wcatcat, &
+ ecorr3_nucl,wcorr3_nucl,ecation_prot,wcatprot,&
+ ecat_prottran,wcat_tran,ecation_protang,wcat_ang,&
+ ecationcation,wcatcat, &
escbase,wscbase,epepbase,wpepbase,escpho,wscpho,epeppho,wpeppho,&
- ecation_nucl,wcatnucl,&
- ecation_nucl,wcatnucl,ehomology_constr,etot
++ ecation_nucl,wcatnucl,ehomology_constr,&
+ elipbond,elipang,eliplj,elipelec,etot
10 format (/'Virtual-chain energies:'// &
'EVDW= ',1pE16.6,' WEIGHT=',1pD16.6,' (SC-SC)'/ &
'EVDW2= ',1pE16.6,' WEIGHT=',1pD16.6,' (SC-p)'/ &
'ESCPHO=',1pE16.6,' WEIGHT=',1pD16.6,'(sc-prot nucl-phosphate)'/&
'EPEPPHO=',1pE16.6,' WEIGHT=',1pD16.6,'(pep-prot nucl-phosphate)'/&
'ECATBASE=',1pE16.6,' WEIGHT=',1pD16.6,'(cation nucl-base)'/&
+ 'H_CONS=',1pE16.6,' (Homology model constraints energy)'/&
+ 'ELIPBOND=',1pE16.6,'(matrini bond energy)'/&
+ 'ELIPANG=',1pE16.6,'(matrini angle energy)'/&
+ 'ELIPLJ=',1pE16.6,'(matrini Lennard-Jones energy)'/&
+ 'ELIPELEC=',1pE16.6,'(matrini electrostatic energy)'/&
'ETOT= ',1pE16.6,' (total)')
#else
write (iout,10) evdw,wsc,evdw2,wscp,ees,welec,&
'ESCPHO=',1pE16.6,' WEIGHT=',1pD16.6,'(sc-prot nucl-phosphate)'/&
'EPEPPHO=',1pE16.6,' WEIGHT=',1pD16.6,'(pep-prot nucl-phosphate)'/&
'ECATBASE=',1pE16.6,' WEIGHT=',1pD16.6,'(cation nucl-base)'/&
+ 'H_CONS=',1pE16.6,' (Homology model constraints energy)'/&
+ 'ELIPBOND=',1pE16.6,'(matrini bond energy)'/&
+ 'ELIPANG=',1pE16.6,'(matrini angle energy)'/&
+ 'ELIPLJ=',1pE16.6,'(matrini Lennard-Jones energy)'/&
+ 'ELIPELEC=',1pE16.6,'(matrini electrostatic energy)'/&
'ETOT= ',1pE16.6,' (total)')
#endif
return
endif
if (energy_dec) write (iout,'(a6,2i5,0pf7.3,2e10.2,e11.3)')&
-- 'evdw',i,j,evdwij,xi,xj,rij !,"egb"
++ 'evdw',i,j,evdwij,1.0D0/rij,1.0D0/rij_shift,dabs(aa/bb)**(1.0D0/6.0D0)!,"egb"
!C print *,i,j,c(1,i),c(1,j),c(2,i),c(2,j),c(3,i),c(3,j)
! if (energy_dec) write (iout,*) &
! 'evdw',i,j,evdwij
! include 'COMMON.CONTROL'
real(kind=8),dimension(3) :: ggg
!el local variables
-- integer :: i,iint,j,k,iteli,itypj,subchap,icont
++ integer :: i,iint,j,k,iteli,itypj,subchap,iconta
real(kind=8) :: evdw2,evdw2_14,xi,yi,zi,xj,yj,zj,rrij,fac,&
e1,e2,evdwij,rij
real(kind=8) :: xj_safe,yj_safe,zj_safe,xj_temp,yj_temp,zj_temp,&
!d write (iout,*) 'iatscp_s=',iatscp_s,' iatscp_e=',iatscp_e
! do i=iatscp_s,iatscp_e
if (nres_molec(1).eq.0) return
-- do icont=g_listscp_start,g_listscp_end
-- i=newcontlistscpi(icont)
-- j=newcontlistscpj(icont)
++ do iconta=g_listscp_start,g_listscp_end
++! print *,"icont",iconta,g_listscp_start,g_listscp_end
++ i=newcontlistscpi(iconta)
++ j=newcontlistscpj(iconta)
if (itype(i,1).eq.ntyp1 .or. itype(i+1,1).eq.ntyp1) cycle
iteli=itel(i)
xi=0.5D0*(c(1,i)+c(1,i+1))
yi=0.5D0*(c(2,i)+c(2,i+1))
zi=0.5D0*(c(3,i)+c(3,i+1))
call to_box(xi,yi,zi)
--
++! print *,itel(i),i,j
! do iint=1,nscp_gr(i)
! do j=iscpstart(i,iint),iscpend(i,iint)
! include 'COMMON.VAR'
! include 'COMMON.INTERACT'
! include 'COMMON.IOUNITS'
-- real(kind=8),dimension(3) :: ggg
++ real(kind=8),dimension(3) :: ggg,vec
!el local variables
-- integer :: i,j,ii,jj,iii,jjj,k
-- real(kind=8) :: fac,eij,rdis,ehpb,dd,waga
++ integer :: i,j,ii,jj,iii,jjj,k,mnumii,mnumjj
++ real(kind=8) :: fac,eij,rdis,ehpb,dd,waga,xi,yi,zi,zj,yj,xj
ehpb=0.0D0
--!d write(iout,*)'edis: nhpb=',nhpb,' fbr=',fbr
--!d write(iout,*)'link_start=',link_start,' link_end=',link_end
++! write(iout,*)'edis: nhpb=',nhpb!,' fbr=',fbr
++! write(iout,*)'link_start=',link_start,' link_end=',link_end
if (link_end.eq.0) return
do i=link_start,link_end
! If ihpb(i) and jhpb(i) > NRES, this is a SC-SC distance, otherwise a
! CA-CA distance used in regularization of structure.
++
ii=ihpb(i)
jj=jhpb(i)
! iii and jjj point to the residues for which the distance is assigned.
iii=ii
jjj=jj
endif
++ do j=1,3
++ vec(j)=c(j,jj)-c(j,ii)
++ enddo
++ mnumii=molnum(iii)
++ mnumjj=molnum(jjj)
++ if (energy_dec) write(iout,*) i,ii,jj,mnumii,mnumjj,itype(jjj,mnumjj),itype(iii,mnumii)
++ if ((itype(iii,mnumii).gt.ntyp_molec(mnumii)).or.(itype(jjj,mnumjj).gt.ntyp_molec(mnumjj))) cycle
++
! write (iout,*) "i",i," ii",ii," iii",iii," jj",jj," jjj",jjj,
! & dhpb(i),dhpb1(i),forcon(i)
! 24/11/03 AL: SS bridges handled separately because of introducing a specific
enddo
else
dd=dist(ii,jj)
++
if (constr_dist.eq.11) then
ehpb=ehpb+fordepth(i)**4.0d0 &
*rlornmr1(dd,dhpb(i),dhpb1(i),forcon(i))
!c write (iout,*) "alph nmr",
!c & dd,2*forcon(i)*gnmr1(dd,dhpb(i),dhpb1(i))
else
++ xi=c(1,ii)
++ yi=c(2,ii)
++ zi=c(3,ii)
++ call to_box(xi,yi,zi)
++ xj=c(1,jj)
++ yj=c(2,jj)
++ zj=c(3,jj)
++ call to_box(xj,yj,zj)
++ xj=boxshift(xj-xi,boxxsize)
++ yj=boxshift(yj-yi,boxysize)
++ zj=boxshift(zj-zi,boxzsize)
++ vec(1)=xj
++ vec(2)=yj
++ vec(3)=zj
++ dd=sqrt(xj*xj+yj*yj+zj*zj)
rdis=dd-dhpb(i)
!C Get the force constant corresponding to this distance.
waga=forcon(i)
!C Calculate the contribution to energy.
ehpb=ehpb+waga*rdis*rdis
++ if (energy_dec) write (iout,'(a6,2i5,5f10.3)') "edis",ii,jj, &
++ ehpb,dd,dhpb(i),waga,rdis
++
!c write (iout,*) "alpha reg",dd,waga*rdis*rdis
!C
!C Evaluate gradient.
endif
do j=1,3
-- ggg(j)=fac*(c(j,jj)-c(j,ii))
++ ggg(j)=fac*vec(j)
enddo
!cd print '(i3,3(1pe14.5))',i,(ggg(j),j=1,3)
!C If this is a SC-SC distance, we need to calculate the contributions to the
! if (.not.allocated(gradbx)) allocate(gradbx(3,nres)) !(3,maxres)
do i=ibondp_start,ibondp_end
++#ifdef FIVEDIAG
++ if (itype(i-1).eq.ntyp1 .or. itype(i).eq.ntyp1) cycle
++ diff = vbld(i)-vbldp0
++#else
if (itype(i-1,1).eq.ntyp1 .and. itype(i,1).eq.ntyp1) cycle
if (itype(i-1,1).eq.ntyp1 .or. itype(i,1).eq.ntyp1) then
!C estr1=estr1+gnmr1(vbld(i),-1.0d0,distchainmax)
else
diff = vbld(i)-vbldp0
endif
++#endif
if (energy_dec) write (iout,'(a7,i5,4f7.3)') &
"estr bb",i,vbld(i),vbldp0,diff,AKP*diff*diff
estr=estr+diff*diff
etors_d=0.0d0
return
end subroutine etor_d
+ !-----------------------------------------------------------------------------
-c LICZENIE WIEZOW Z ROWNANIA ENERGII MODELLERA
++!c LICZENIE WIEZOW Z ROWNANIA ENERGII MODELLERA
+ subroutine e_modeller(ehomology_constr)
+ real(kind=8) :: ehomology_constr
+ ehomology_constr=0.0d0
+ write (iout,*) "!!!!!UWAGA, JESTEM W DZIWNEJ PETLI, TEST!!!!!"
+ return
+ end subroutine e_modeller
+ C !!!!!!!! NIE CZYTANE !!!!!!!!!!!
#else
!-----------------------------------------------------------------------------
subroutine etor(etors)
gradvalst2,etori
logical lprn
integer :: i,j,itori,itori1,nval,k,l
--
++! lprn=.true.
if (lprn) write (iout,*) "etor_kcc tor_mode",tor_mode
etors=0.0D0
do i=iphi_start,iphi_end
sint2,xp,yp,xxp,yyp,zzp,dj
! common /przechowalnia/ fromto
++#ifdef FIVEDIAG
++ if(.not. allocated(fromto)) allocate(fromto(3,3))
++#else
if(.not. allocated(fromto)) allocate(fromto(3,3,maxdim))
++#endif
! get the position of the jth ijth fragment of the chain coordinate system
! in the fromto array.
! indmat(i,j)=((2*(nres-2)-i)*(i-1))/2+j-1
!
! generate the matrix products of type r(i)t(i)...r(j)t(j)
!
++#ifndef FIVEDIAG
do i=2,nres-2
ind=indmat(i,i+1)
do k=1,3
fromto(k,l,ind)=temp(k,l)
enddo
enddo
++
do j=i+1,nres-2
ind=indmat(i,j+1)
do k=1,3
enddo
enddo
enddo
++#endif
!
! Calculate derivatives.
!
ind1=ind1+1
ind=indmat(i+1,j+1)
!d print *,'i=',i,' j=',j,' ind=',ind,' ind1=',ind1
++#ifdef FIVEDIAG
++ call build_fromto(i+1,j+1,fromto)
++c write(iout,'(7hfromto 9f10.5)')((fromto(k,l),l=1,3),k=1,3)
++ do k=1,3
++ do l=1,3
++ tempkl=0.0D0
++ do m=1,2
++ tempkl=tempkl+prordt(k,m,i)*fromto(m,l)
++ enddo
++ temp(k,l)=tempkl
++ enddo
++ enddo
++#else
do k=1,3
do l=1,3
tempkl=0.0D0
temp(k,l)=tempkl
enddo
enddo
++#endif
!d print '(9f8.3)',((fromto(k,l,ind),l=1,3),k=1,3)
!d print '(9f8.3)',((prod(k,l,i),l=1,3),k=1,3)
!d print '(9f8.3)',((temp(k,l),l=1,3),k=1,3)
!
!--- Calculate the derivatives in phi
!
++#ifdef FIVEDIAG
++ do k=1,3
++ do l=1,3
++ tempkl=0.0D0
++ do m=1,3
++ tempkl=tempkl+prodrt(k,m,i)*fromto(m,l)
++ enddo
++ temp(k,l)=tempkl
++ enddo
++ enddo
++#else
do k=1,3
do l=1,3
tempkl=0.0D0
temp(k,l)=tempkl
enddo
enddo
++#endif
++
++
do k=1,3
dcdv(k+3,ind1)=vbld(i+1)*temp(k,1)
enddo
xx(2)=yyp*r(2,2,i-1)+zzp*r(2,3,i-1)
xx(3)=yyp*r(3,2,i-1)+zzp*r(3,3,i-1)
do k=1,3
- dj=0.0D0
+ dj=0.0D0
+ do l=1,3
+ dj=dj+prod(k,l,i-1)*xx(l)
+ enddo
+ dxds(jjj+k,i)=dj
+ enddo
+ jjj=jjj+3
+ enddo
+ enddo
+ return
+ end subroutine cartder
++#ifdef FIVEDIAG
++ subroutine build_fromto(i,j,fromto)
++ implicit none
++ integer i,j,jj,k,l,m
++ double precision fromto(3,3),temp(3,3),dp(3,3)
++ double precision dpkl
++ save temp
++!
++! generate the matrix products of type r(i)t(i)...r(j)t(j) on the fly
++!
++! write (iout,*) "temp on entry"
++! write (iout,'(3f10.5)') ((temp(k,l),l=1,3),k=1,3)
++! do i=2,nres-2
++! ind=indmat(i,i+1)
++ if (j.eq.i+1) then
++ do k=1,3
++ do l=1,3
++ temp(k,l)=rt(k,l,i)
++ enddo
++ enddo
++ do k=1,3
+ do l=1,3
- dj=dj+prod(k,l,i-1)*xx(l)
++ fromto(k,l)=temp(k,l)
++ enddo
++ enddo
++ else
++! do j=i+1,nres-2
++! ind=indmat(i,j+1)
++ do k=1,3
++ do l=1,3
++ dpkl=0.0d0
++ do m=1,3
++ dpkl=dpkl+temp(k,m)*rt(m,l,j-1)
++ enddo
++ dp(k,l)=dpkl
++ fromto(k,l)=dpkl
+ enddo
- dxds(jjj+k,i)=dj
+ enddo
- jjj=jjj+3
- enddo
- enddo
++ do k=1,3
++ do l=1,3
++ temp(k,l)=dp(k,l)
++ enddo
++ enddo
++ endif
++! write (iout,*) "temp upon exit"
++! write (iout,'(3f10.5)') ((temp(k,l),l=1,3),k=1,3)
++! enddo
++! enddo
+ return
- end subroutine cartder
++ end subroutine build_fromto
++#endif
++
!-----------------------------------------------------------------------------
! checkder_p.F
!-----------------------------------------------------------------------------
if (itypj.eq.ntyp1) cycle
! dscj_inv=dsc_inv(itypj)
dscj_inv=vbld_inv(j+nres)
--chi1=chi(itypi,itypj)
--chi2=chi(itypj,itypi)
--chi12=chi1*chi2
--chip1=chip(itypi)
++!chi1=chi(itypi,itypj)
++!chi2=chi(itypj,itypi)
++!chi12=chi1*chi2
++!chip1=chip(itypi)
alf1=alp(itypi)
alf2=alp(itypj)
alf12=0.5D0*(alf1+alf2)
!
! Calculate the disulfide-bridge and other energy and the contributions
! from other distance constraints.
-- call edis(ehpb)
++! call edis(ehpb)
!
! Calculate the virtual-bond-angle energy.
!
!#undef DEBUG
return
end subroutine cartgrad
++
++#ifdef FIVEDIAG
++ subroutine grad_transform
++ implicit none
++#ifdef MPI
++ include 'mpif.h'
++#endif
++ integer i,j,kk
++#ifdef DEBUG
++ write (iout,*)"Converting virtual-bond gradient to CA/SC gradient"
++ write (iout,*) "dC/dX gradient"
++ do i=0,nres
++ write (iout,'(i5,3f10.5,5x,3f10.5)') i,(gcart(j,i),j=1,3),
++ & (gxcart(j,i),j=1,3)
++ enddo
++#endif
++ do i=nres,1,-1
++ do j=1,3
++ gcart(j,i)=-gcart(j,i)+gcart(j,i-1)-gxcart(j,i)
++! gcart_new(j,i)=-gcart(j,i)+gcart(j,i-1)-gxcart(j,i)
++ enddo
++! write (iout,'(i5,3f10.5,5x,3f10.5,5x,3f10.5)') i,(gcart(j,i),j=1,3), &
++! (gcart_new(j,i),j=1,3),(gxcart(j,i),j=1,3)
++ enddo
++! Correction: dummy residues
++ do i=2,nres
++ if (itype(i-1).eq.ntyp1 .and. itype(i).ne.ntyp1) then
++ gcart(:,i)=gcart(:,i)+gcart(:,i-1)
++ else if (itype(i-1).ne.ntyp1 .and. itype(i).eq.ntyp1) then
++ gcart(:,i-1)=gcart(:,i-1)+gcart(:,i)
++ endif
++ enddo
++c if (nnt.gt.1) then
++c do j=1,3
++c gcart(j,nnt)=gcart(j,nnt)+gcart(j,1)
++c enddo
++c endif
++c if (nct.lt.nres) then
++c do j=1,3
++c! gcart_new(j,nct)=gcart_new(j,nct)+gcart_new(j,nres)
++c gcart(j,nct)=gcart(j,nct)+gcart(j,nres)
++c enddo
++c endif
++#ifdef DEBUG
++ write (iout,*) "CA/SC gradient"
++ do i=1,nres
++ write (iout,'(i5,3f10.5,5x,3f10.5)') i,(gcart(j,i),j=1,3),
++ & (gxcart(j,i),j=1,3)
++ enddo
++#endif
++ return
++ end subroutine grad_transform
++#endif
++
!-----------------------------------------------------------------------------
subroutine zerograd
- ! implicit real*8 (a-h,o-z)
+ ! implicit real(kind=8) (a-h,o-z)
! include 'DIMENSIONS'
! include 'COMMON.DERIV'
! include 'COMMON.CHAIN'
gvdwc_peppho(j,i)=0.0d0
gradnuclcatx(j,i)=0.0d0
gradnuclcat(j,i)=0.0d0
+ gradlipbond(j,i)=0.0d0
+ gradlipang(j,i)=0.0d0
+ gradliplj(j,i)=0.0d0
+ gradlipelec(j,i)=0.0d0
+ gradcattranc(j,i)=0.0d0
+ gradcattranx(j,i)=0.0d0
+ gradcatangx(j,i)=0.0d0
+ gradcatangc(j,i)=0.0d0
+ duscdiff(j,i)=0.0d0
+ duscdiffx(j,i)=0.0d0
enddo
enddo
do i=0,nres
end subroutine calctube2
!=====================================================================================================================================
subroutine calcnano(Etube)
-- real(kind=8),dimension(3) :: vectube
++ use MD_data, only:totTafm
++ real(kind=8),dimension(3) :: vectube,cm
real(kind=8) :: Etube,xtemp,xminact,yminact,&
ytemp,xmin,ymin,tub_r,rdiff,rdiff6,fac,denominator,faccav,&
-- sc_aa_tube,sc_bb_tube,zmin,ztemp,zminact
-- integer:: i,j,iti,r
--
++ sc_aa_tube,sc_bb_tube,zmin,ztemp,zminact,tubezcenter,xi,yi,zi!,&
++! vecsim,vectrue
++ real(kind=8) :: eps,sig,aa_tub_lip,bb_tub_lip
++ integer:: i,j,iti,r,ilol,ityp
++! totTafm=2.0
Etube=0.0d0
++ call to_box(tubecenter(1),tubecenter(2),tubecenter(3))
! print *,itube_start,itube_end,"poczatek"
do i=itube_start,itube_end
enetube(i)=0.0d0
!C lets ommit dummy atoms for now
if ((itype(i,1).eq.ntyp1).or.(itype(i+1,1).eq.ntyp1)) cycle
!C now calculate distance from center of tube and direction vectors
-- xmin=boxxsize
-- ymin=boxysize
-- zmin=boxzsize
--
-- do j=-1,1
-- vectube(1)=dmod((c(1,i)+c(1,i+1))/2.0d0,boxxsize)
-- vectube(1)=vectube(1)+boxxsize*j
-- vectube(2)=dmod((c(2,i)+c(2,i+1))/2.0d0,boxysize)
-- vectube(2)=vectube(2)+boxysize*j
-- vectube(3)=dmod((c(3,i)+c(3,i+1))/2.0d0,boxzsize)
-- vectube(3)=vectube(3)+boxzsize*j
--
-
- xminact=dabs(vectube(1)-tubecenter(1))
- yminact=dabs(vectube(2)-tubecenter(2))
- zminact=dabs(vectube(3)-tubecenter(3))
- if (xmin.gt.xminact) then
- xmin=xminact
- xtemp=vectube(1)
- endif
- if (ymin.gt.yminact) then
- ymin=yminact
- ytemp=vectube(2)
- endif
- if (zmin.gt.zminact) then
- zmin=zminact
- ztemp=vectube(3)
- endif
- enddo
- vectube(1)=xtemp
- vectube(2)=ytemp
- vectube(3)=ztemp
- xminact=dabs(vectube(1)-tubecenter(1))
- yminact=dabs(vectube(2)-tubecenter(2))
- zminact=dabs(vectube(3)-tubecenter(3))
-
- if (xmin.gt.xminact) then
- xmin=xminact
- xtemp=vectube(1)
- endif
- if (ymin.gt.yminact) then
- ymin=yminact
- ytemp=vectube(2)
- endif
- if (zmin.gt.zminact) then
- zmin=zminact
- ztemp=vectube(3)
- endif
- enddo
- vectube(1)=xtemp
- vectube(2)=ytemp
- vectube(3)=ztemp
++! do j=-1,1
++ xi=(c(1,i)+c(1,i+1))/2.0d0
++ yi=(c(2,i)+c(2,i+1))/2.0d0
++ zi=((c(3,i)+c(3,i+1))/2.0d0)
++ call to_box(xi,yi,zi)
++! tubezcenter=totTafm*velNANOconst+tubecenter(3)
-- vectube(1)=vectube(1)-tubecenter(1)
-- vectube(2)=vectube(2)-tubecenter(2)
-- vectube(3)=vectube(3)-tubecenter(3)
++ vectube(1)=boxshift(xi-tubecenter(1),boxxsize)
++ vectube(2)=boxshift(yi-tubecenter(2),boxysize)
++ vectube(3)=boxshift(zi-tubecenter(3),boxzsize)
!C print *,"x",(c(1,i)+c(1,i+1))/2.0d0,tubecenter(1)
!C print *,"y",(c(2,i)+c(2,i+1))/2.0d0,tubecenter(2)
!C in UNRES uncomment the line below as GLY has no side-chain...
!C .or.(iti.eq.10)
) cycle
-- xmin=boxxsize
-- ymin=boxysize
-- zmin=boxzsize
-- do j=-1,1
-- vectube(1)=dmod((c(1,i+nres)),boxxsize)
-- vectube(1)=vectube(1)+boxxsize*j
-- vectube(2)=dmod((c(2,i+nres)),boxysize)
-- vectube(2)=vectube(2)+boxysize*j
-- vectube(3)=dmod((c(3,i+nres)),boxzsize)
-- vectube(3)=vectube(3)+boxzsize*j
--
++ xi=c(1,i+nres)
++ yi=c(2,i+nres)
++ zi=c(3,i+nres)
++ call to_box(xi,yi,zi)
++ tubezcenter=totTafm*velNANOconst+tubecenter(3)
-- xminact=dabs(vectube(1)-tubecenter(1))
-- yminact=dabs(vectube(2)-tubecenter(2))
-- zminact=dabs(vectube(3)-tubecenter(3))
++ vectube(1)=boxshift(xi-tubecenter(1),boxxsize)
++ vectube(2)=boxshift(yi-tubecenter(2),boxysize)
++ vectube(3)=boxshift(zi-tubecenter(3),boxzsize)
-- if (xmin.gt.xminact) then
-- xmin=xminact
-- xtemp=vectube(1)
-- endif
-- if (ymin.gt.yminact) then
-- ymin=yminact
-- ytemp=vectube(2)
-- endif
-- if (zmin.gt.zminact) then
-- zmin=zminact
-- ztemp=vectube(3)
-- endif
-- enddo
-- vectube(1)=xtemp
-- vectube(2)=ytemp
-- vectube(3)=ztemp
--!C write(iout,*), "tututu", vectube(1),tubecenter(1),vectube(2),
--!C & tubecenter(2)
-- vectube(1)=vectube(1)-tubecenter(1)
-- vectube(2)=vectube(2)-tubecenter(2)
-- vectube(3)=vectube(3)-tubecenter(3)
!C now calculte the distance
tub_r=dsqrt(vectube(1)**2+vectube(2)**2+vectube(3)**2)
!C now normalize vector
if (energy_dec) write(iout,*),i,rdiff,enetube(i+nres),enecavtube(i+nres)
enddo
--
++
do i=itube_start,itube_end
Etube=Etube+enetube(i)+enetube(i+nres)+enecavtube(i) &
+enecavtube(i+nres)
enddo
++
++ do i=ilipbond_start_tub,ilipbond_end_tub
++ ityp=itype(i,4)
++! print *,"ilipbond_start",ilipbond_start,i,ityp
++ if (ityp.gt.ntyp_molec(4)) cycle
++!C now calculate distance from center of tube and direction vectors
++ eps=lip_sig(ityp,18)*4.0d0
++ sig=lip_sig(ityp,18)
++ aa_tub_lip=eps/(sig**12)
++ bb_tub_lip=eps/(sig**6)
++! do j=-1,1
++ xi=c(1,i)
++ yi=c(2,i)
++ zi=c(3,i)
++ call to_box(xi,yi,zi)
++! tubezcenter=totTafm*velNANOconst+tubecenter(3)
++
++ vectube(1)=boxshift(xi-tubecenter(1),boxxsize)
++ vectube(2)=boxshift(yi-tubecenter(2),boxysize)
++ vectube(3)=boxshift(zi-tubecenter(3),boxzsize)
++
++!C print *,"x",(c(1,i)+c(1,i+1))/2.0d0,tubecenter(1)
++!C print *,"y",(c(2,i)+c(2,i+1))/2.0d0,tubecenter(2)
++!C as the tube is infinity we do not calculate the Z-vector use of Z
++!C as chosen axis
++!C vectube(3)=0.0d0
++!C now calculte the distance
++ tub_r=dsqrt(vectube(1)**2+vectube(2)**2+vectube(3)**2)
++!C now normalize vector
++ vectube(1)=vectube(1)/tub_r
++ vectube(2)=vectube(2)/tub_r
++ vectube(3)=vectube(3)/tub_r
++!C calculte rdiffrence between r and r0
++ rdiff=tub_r-tubeR0
++!C and its 6 power
++ rdiff6=rdiff**6.0d0
++!C for vectorization reasons we will sumup at the end to avoid depenence of previous
++ enetube(i)=aa_tub_lip/rdiff6**2.0d0+bb_tub_lip/rdiff6
++ Etube=Etube+enetube(i)
++!C write(iout,*) "TU13",i,rdiff6,enetube(i)
++!C print *,rdiff,rdiff6,pep_aa_tube
++!C pep_aa_tube and pep_bb_tube are precomputed values A=4eps*sigma^12 B=4eps*sigma^6
++!C now we calculate gradient
++ fac=(-12.0d0*aa_tub_lip/rdiff6- &
++ 6.0d0*bb_tub_lip)/rdiff6/rdiff
++ do j=1,3
++ gg_tube(j,i-1)=gg_tube(j,i-1)+vectube(j)*fac
++ enddo
++ if (energy_dec) write(iout,*),i,rdiff,enetube(i+nres)
++ enddo
++
++
++!-----------------------------------------------------------------------
++ if (fg_rank.eq.0) then
++ if (velNANOconst.ne.0) then
++ do j=1,3
++ cm(j)=0.0d0
++ enddo
++ do i=1,inanomove
++ ilol=inanotab(i)
++ do j=1,3
++ cm(j)=cm(j)+c(j,ilol)
++ enddo
++ enddo
++ do j=1,3
++ cm(j)=cm(j)/inanomove
++ enddo
++ vecsim=velNANOconst*totTafm+distnanoinit
++ vectrue=cm(3)-tubecenter(3)
++ etube=etube+0.5d0*forcenanoconst*( vectrue-vecsim)**2
++ fac=forcenanoconst*(vectrue-vecsim)/inanomove
++ do i=1,inanomove
++ ilol=inanotab(i)
++ gg_tube(3,ilol-1)=gg_tube(3,ilol-1)+fac
++ enddo
++ endif
++ endif
! do i=1,20
! print *,"begin", i,"a"
! do r=1,10000
! SOUBROUTINE FOR AFM
subroutine AFMvel(Eafmforce)
use MD_data, only:totTafm
-- real(kind=8),dimension(3) :: diffafm
++ real(kind=8),dimension(3) :: diffafm,cbeg,cend
real(kind=8) :: afmdist,Eafmforce
-- integer :: i
++ integer :: i,j
!C Only for check grad COMMENT if not used for checkgrad
!C totT=3.0d0
!C--------------------------------------------------------
!C print *,"wchodze"
afmdist=0.0d0
Eafmforce=0.0d0
++ cbeg=0.0d0
++ cend=0.0d0
++ if (afmbeg.eq.-1) then
++ do i=1,nbegafmmat
++ do j=1,3
++ cbeg(j)=cbeg(j)+c(j,afmbegcentr(i))/nbegafmmat
++ enddo
++ enddo
++ else
++ do j=1,3
++ cbeg(j)=c(j,afmend)
++ enddo
++ endif
++ if (afmend.eq.-1) then
++ do i=1,nendafmmat
++ do j=1,3
++ cend(j)=cend(j)+c(j,afmendcentr(i))/nendafmmat
++ enddo
++ enddo
++ else
++ cend(j)=c(j,afmend)
++ endif
++
do i=1,3
-- diffafm(i)=c(i,afmend)-c(i,afmbeg)
++ diffafm(i)=cend(i)-cbeg(i)
afmdist=afmdist+diffafm(i)**2
enddo
afmdist=dsqrt(afmdist)
Eafmforce=0.5d0*forceAFMconst &
*(distafminit+totTafm*velAFMconst-afmdist)**2
!C Eafmforce=-forceAFMconst*(dist-distafminit)
++ if (afmend.eq.-1) then
++ do i=1,nendafmmat
++ do j=1,3
++ gradafm(j,afmendcentr(i)-1)=-forceAFMconst* &
++ (distafminit+totTafm*velAFMconst-afmdist) &
++ *diffafm(j)/afmdist/nendafmmat
++ enddo
++ enddo
++ else
do i=1,3
gradafm(i,afmend-1)=-forceAFMconst* &
(distafminit+totTafm*velAFMconst-afmdist) &
*diffafm(i)/afmdist
++ enddo
++ endif
++ if (afmbeg.eq.-1) then
++ do i=1,nbegafmmat
++ do j=1,3
++ gradafm(i,afmbegcentr(i)-1)=forceAFMconst* &
++ (distafminit+totTafm*velAFMconst-afmdist) &
++ *diffafm(i)/afmdist
++ enddo
++ enddo
++ else
++ do i=1,3
gradafm(i,afmbeg-1)=forceAFMconst* &
(distafminit+totTafm*velAFMconst-afmdist) &
*diffafm(i)/afmdist
enddo
++ endif
! print *,'AFM',Eafmforce,totTafm*velAFMconst,afmdist
return
end subroutine AFMvel
!c------------------------------------------------------------------------------
#endif
subroutine ecatcat(ecationcation)
-- integer :: i,j,itmp,xshift,yshift,zshift,subchap,k,itypi,itypj
++ use MD_data, only: t_bath
++ integer :: i,j,itmp,xshift,yshift,zshift,subchap,k,itypi,itypj,irdiff
real(kind=8) :: xi,yi,zi,xj,yj,zj,ract,rcat0,epscalc,r06,r012,&
r7,r4,ecationcation,k0,rcal,aa,bb,sslipi,ssgradlipi,sslipj,ssgradlipj
-- real(kind=8) xj_temp,yj_temp,zj_temp,xj_safe,yj_safe,zj_safe, &
++ real(kind=8) :: xj_temp,yj_temp,zj_temp,xj_safe,yj_safe,zj_safe, &
dist_init,dist_temp,Evan1cat,Evan2cat,Eeleccat
++ real(kind=8) :: awat,bwat,cwat,dwat,sss2min2,sss2mingrad2,rdiff,ewater
real(kind=8),dimension(3) ::dEvan1Cmcat,dEvan2Cmcat,dEeleccat,&
gg,r
zj=boxshift(zj-zi,boxzsize)
rcal =xj**2+yj**2+zj**2
ract=sqrt(rcal)
++ if ((itypi.gt.1).or.(itypj.gt.1)) then
++
! rcat0=3.472
! epscalc=0.05
! r06 = rcat0**6
r012,rcal**6,ichargecat(itypi)*ichargecat(itypj)
! write(iout,*) "ecatcat",i,j, ecationcation,xj,yj,zj
ecationcation=ecationcation+Evan1cat+Evan2cat+Eeleccat
++ else !this is water part and other non standard molecules
++
++ sss2min2=sscale2(ract,10.0d0,1.0d0)! cutoff for water interaction is 15A
++ if (sss2min2.eq.0.0d0) cycle
++ sss2mingrad2=sscagrad2(ract,10.0d0,1.0d0)
++ irdiff=int((ract-2.06d0)*50.0d0)+1
++
++ rdiff=ract-((irdiff-1)*0.02d0+2.06d0)
++ if (irdiff.le.0) then
++ irdiff=0
++ rdiff=ract
++ endif
++! print *,rdiff,ract,irdiff,sss2mingrad2
++ awat=awaterenta(irdiff)-awaterentro(irdiff)*t_bath/1000.0d0
++ bwat=bwaterenta(irdiff)-bwaterentro(irdiff)*t_bath/1000.0d0
++ cwat=cwaterenta(irdiff)-cwaterentro(irdiff)*t_bath/1000.0d0
++ dwat=dwaterenta(irdiff)-dwaterentro(irdiff)*t_bath/1000.0d0
++ r(1)=xj
++ r(2)=yj
++ r(3)=zj
++
++ ewater=awat+bwat*rdiff+cwat*rdiff*rdiff+dwat*rdiff*rdiff*rdiff
++ ecationcation=ecationcation+ewater*sss2min2
++ do k=1,3
++ gg(k)=(bwat+2.0d0*cwat*rdiff+dwat*3.0d0*rdiff*rdiff)*r(k)/ract
++ gradcatcat(k,i)=gradcatcat(k,i)-gg(k)*sss2min2-sss2mingrad2*ewater*r(k)/ract
++ gradcatcat(k,j)=gradcatcat(k,j)+gg(k)*sss2min2+sss2mingrad2*ewater*r(k)/ract
++ enddo
++ if (energy_dec) write(iout,'(2f10.7,f15.7,2i5)') rdiff,ract,ecationcation,i,j
++ endif ! end water
enddo
enddo
return
! chis2 = chis(itypj,itypi)
chis12 = chis1 * chis2
sig1 = sigmap1cat(itypi,itypj)
++ sig2=0.0d0
! sig2 = sigmap2(itypi,itypj)
! alpha factors from Fcav/Gcav
b1cav = alphasurcat(1,itypi,itypj)
1.0d0/rij,Rtail,Rhead,evdwij,Fcav,Ecl,Egb,Epol,Fisocav,Elj,&
Equad,evdwij+Fcav+eheadtail,evdw
! evdw = evdw + Fcav + eheadtail
++ if (energy_dec) write(iout,*) "FCAV", &
++ sig1,sig2,b1cav,b2cav,b3cav,b4cav
! print *,"before sc_grad_cat", i,j, gradpepcat(1,j)
! iF (nstate(itypi,itypj).eq.1) THEN
CALL sc_grad_cat
! chis2 = chis(itypj,itypi)
chis12 = chis1 * chis2
sig1 = sigmap1cat(itypi,itypj)
++ sig2=0.0
! sig2 = sigmap2(itypi,itypj)
! alpha factors from Fcav/Gcav
b1cav = alphasurcat(1,itypi,itypj)
! use comm_momo
integer i,j,k,subchap,itmp,inum
real(kind=8) :: xi,yi,zi,xj,yj,zj,ract,rcat0,epscalc,r06,r012,&
-- r7,r4,ecationcation
++ r7,r4
real(kind=8) xj_temp,yj_temp,zj_temp,xj_safe,yj_safe,zj_safe, &
dist_init,dist_temp,ecation_prot,rcal,rocal, &
Evan1,Evan2,EC,cm1mag,DASGL,delta,r0p,Epepcat, &
dGCLdOM1 = 0.0d0
dGCLdOM2 = 0.0d0
dGCLdOM12 = 0.0d0
++
ee0 = dexp(-( Rhead_sq ) / (4.0d0 * a12sq))
Fgb = sqrt( ( Rhead_sq ) + a12sq * ee0)
debkap=debaykapcat(itypi,itypj)
++ if (energy_dec) write(iout,*) "egb",Qij,debkap,Fgb,a12sq,ee0
Egb = -(332.0d0 * Qij *&
(1.0/eps_in-dexp(-debkap*Fgb)/eps_out)) / Fgb
! print *,"EGB WTF",Qij,eps_inout_fac,Fgb,itypi,itypj,eps_in,eps_out
gradtschebyshev=aux
return
end function gradtschebyshev
+!!!!!!!!!--------------------------------------------------------------
+ subroutine lipid_bond(elipbond)
+ real(kind=8) :: elipbond,fac,dist_sub,sumdist
+ real(kind=8), dimension(3):: dist
+ integer(kind=8) :: i,j,k,ibra,ityp,jtyp,ityp1
+ elipbond=0.0d0
+! print *,"before",ilipbond_start,ilipbond_end
+ do i=ilipbond_start,ilipbond_end
+! print *,i,i+1,"i,i+1"
+ ityp=itype(i,4)
+ ityp1=itype(i+1,4)
+! print *,ityp,ityp1,"itype"
+ j=i+1
+ if (ityp.eq.12) ibra=i
+ if ((ityp.eq.ntyp1_molec(4)).or.(ityp1.ge.ntyp1_molec(4)-1)) cycle
+ if (ityp.eq.(ntyp1_molec(4)-1)) then
+ !cofniecie do ostatnie GL1
+! i=ibra
+ j=ibra
+ else
+ j=i
+ endif
+ jtyp=itype(j,4)
+ do k=1,3
+ dist(k)=c(k,j)-c(k,i+1)
+ enddo
+ sumdist=0.0d0
+ do k=1,3
+ sumdist=sumdist+dist(k)**2
+ enddo
+ dist_sub=sqrt(sumdist)
+! print *,"before",i,j,ityp1,ityp,jtyp
+ elipbond=elipbond+kbondlip*((dist_sub-lip_bond(jtyp,ityp1))**2)
+ fac=kbondlip*(dist_sub-lip_bond(jtyp,ityp1))
+ do k=1,3
+ gradlipbond(k,i+1)= gradlipbond(k,i+1)-fac*dist(k)/dist_sub
+ gradlipbond(k,j)=gradlipbond(k,j)+fac*dist(k)/dist_sub
+ enddo
+ if (energy_dec) write(iout,*) "lipbond",j,i+1,dist_sub,lip_bond(jtyp,ityp1),kbondlip,fac
+ enddo
+ elipbond=elipbond*0.5d0
+ return
+ end subroutine lipid_bond
+!---------------------------------------------------------------------------------------
+ subroutine lipid_angle(elipang)
+ real(kind=8) :: elipang,alfa,xa(3),xb(3),alfaact,alfa0,force,fac,&
+ scalara,vnorm,wnorm,sss,sss_grad,eangle
+ integer :: i,j,k,l,m,ibra,ityp1,itypm1,itypp1
+ elipang=0.0d0
+! print *,"ilipang_start,ilipang_end",ilipang_start,ilipang_end
+ do i=ilipang_start,ilipang_end
+! do i=4,4
+
+! the loop is centered on the central residue
+ itypm1=itype(i-1,4)
+ ityp1=itype(i,4)
+ itypp1=itype(i+1,4)
+! print *,i,i,j,"processor",fg_rank
+ j=i-1
+ k=i
+ l=i+1
+ if (ityp1.eq.12) ibra=i
+ if ((itypm1.eq.ntyp1_molec(4)).or.(ityp1.eq.ntyp1_molec(4))&
+ .or.(itypp1.eq.ntyp1_molec(4))) cycle !cycle if any of the angles is dummy
+ if ((itypm1.eq.ntyp1_molec(4)-1).or.(itypp1.eq.ntyp1_molec(4)-1)) cycle
+ ! branching is only to one angle
+ if (ityp1.eq.ntyp1_molec(4)-1) then
+ k=ibra
+ j=ibra-1
+ endif
+ itypm1=itype(j,4)
+ ityp1=itype(k,4)
+ do m=1,3
+ xa(m)=c(m,j)-c(m,k)
+ xb(m)=c(m,l)-c(m,k)
+! xb(m)=1.0d0
+ enddo
+ vnorm=dsqrt(xa(1)*xa(1)+xa(2)*xa(2)+xa(3)*xa(3))
+ wnorm=dsqrt(xb(1)*xb(1)+xb(2)*xb(2)+xb(3)*xb(3))
+ scalara=(xa(1)*xb(1)+xa(2)*xb(2)+xa(3)*xb(3))/(vnorm*wnorm)
+! if (((scalar*scalar).gt.0.99999999d0).and.(alfa0.eq.180.0d0)) cycle
+
+ alfaact=scalara
+! sss=sscale_martini_angle(alfaact)
+! sss_grad=sscale_grad_martini_angle(alfaact)
+! print *,sss_grad,"sss_grad",sss
+! if (sss.le.0.0) cycle
+! if (sss_grad.ne.0.0) print *,sss_grad,"sss_grad"
+ force=lip_angle_force(itypm1,ityp1,itypp1)
+ alfa0=lip_angle_angle(itypm1,ityp1,itypp1)
+ eangle=force*(alfaact-dcos(alfa0))*(alfaact-dcos(alfa0))*0.5d0
+ elipang=elipang+eangle!*(1001.0d0-1000.0d0*sss)
+ fac=force*(alfaact-dcos(alfa0))!*(1001.0d0-1000.0d0*sss)-sss_grad*eangle*1000.0d0
+ do m=1,3
+ gradlipang(m,j)=gradlipang(m,j)+(fac &!/dsqrt(1.0d0-scalar*scalar)&
+ *(xb(m)-scalara*wnorm*xa(m)/vnorm)&
+ /(vnorm*wnorm))!-sss_grad*eangle*xa(m)/vnorm
- subroutine make_SCSC_inter_list
- include 'mpif.h'
- real*8 :: xi,yi,zi,xj,yj,zj,xj_safe,yj_safe,zj_safe,xj_temp,yj_temp,zj_temp
- real*8 :: dist_init, dist_temp,r_buff_list
- integer:: contlisti(250*nres),contlistj(250*nres)
-! integer :: newcontlisti(200*nres),newcontlistj(200*nres)
- integer i,j,itypi,itypj,subchap,xshift,yshift,zshift,iint,ilist_sc,g_ilist_sc
- integer displ(0:nprocs),i_ilist_sc(0:nprocs),ierr
-! print *,"START make_SC"
- r_buff_list=5.0
- ilist_sc=0
- do i=iatsc_s,iatsc_e
- itypi=iabs(itype(i,1))
- if (itypi.eq.ntyp1) cycle
- xi=c(1,nres+i)
- yi=c(2,nres+i)
- zi=c(3,nres+i)
- call to_box(xi,yi,zi)
- do iint=1,nint_gr(i)
-! print *,"is it wrong", iint,i
- do j=istart(i,iint),iend(i,iint)
- itypj=iabs(itype(j,1))
- if (energy_dec) write(iout,*) "LISTA ZAKRES",istart(i,iint),iend(i,iint),iatsc_s,iatsc_e
- if (itypj.eq.ntyp1) cycle
- xj=c(1,nres+j)
- yj=c(2,nres+j)
- zj=c(3,nres+j)
- call to_box(xj,yj,zj)
-! call lipid_layer(xj,yj,zj,sslipj,ssgradlipj)
-! faclipij2=(sslipi+sslipj)/2.0d0*lipscale**2+1.0d0
+ gradlipang(m,l)=gradlipang(m,l)+(fac & !/dsqrt(1.0d0-scalar*scalar)&
+ *(xa(m)-scalara*vnorm*xb(m)/wnorm)&
+ /(vnorm*wnorm))!+sss_grad*eangle*xb(m)/wnorm
+
+ gradlipang(m,k)=gradlipang(m,k)-(fac)& !/dsqrt(1.0d0-scalar*scalar)&
+ *(xb(m)-scalara*wnorm*xa(m)/vnorm)&
+ /((vnorm*wnorm))-(fac & !/dsqrt(1.0d0-scalar*scalar)&
+ *(xa(m)-scalara*vnorm*xb(m)/wnorm)&
+ /(vnorm*wnorm))!-sss_grad*eangle*xa(m)/vnorm&
+ !-sss_grad*eangle*xb(m)/wnorm
+
+
+! *(xb(m)*vnorm*wnorm)&
+
+!-xa(m)*xa(m)*xb(m)*wnorm/vnorm)&
+ enddo
+ if (energy_dec) write(iout,*) "elipang",j,k,l,force,alfa0,alfaact,elipang
+ enddo
+ return
+ end subroutine lipid_angle
+!--------------------------------------------------------------------
+ subroutine lipid_lj(eliplj)
+ real(kind=8) :: eliplj,fac,sumdist,dist_sub,LJ1,LJ2,LJ,&
+ xj,yj,zj,xi,yi,zi,sss,sss_grad
+ real(kind=8), dimension(3):: dist
+ integer :: i,j,k,inum,ityp,jtyp
++ eliplj=0.0d0
+ do inum=iliplj_start,iliplj_end
+ i=mlipljlisti(inum)
+ j=mlipljlistj(inum)
+! print *,inum,i,j,"processor",fg_rank
+ ityp=itype(i,4)
+ jtyp=itype(j,4)
+ xi=c(1,i)
+ yi=c(2,i)
+ zi=c(3,i)
+ call to_box(xi,yi,zi)
+ xj=c(1,j)
+ yj=c(2,j)
+ zj=c(3,j)
+ call to_box(xj,yj,zj)
+ xj=boxshift(xj-xi,boxxsize)
+ yj=boxshift(yj-yi,boxysize)
+ zj=boxshift(zj-zi,boxzsize)
+ dist(1)=xj
+ dist(2)=yj
+ dist(3)=zj
+ ! do k=1,3
+ ! dist(k)=c(k,j)-c(k,i)
+ ! enddo
+ sumdist=0.0d0
+ do k=1,3
+ sumdist=sumdist+dist(k)**2
+ enddo
+
+ dist_sub=sqrt(sumdist)
+ sss=sscale_martini(dist_sub)
+ if (energy_dec) write(iout,*) "LJ LIP bef",i,j,ityp,jtyp,dist_sub
+ if (sss.le.0.0) cycle
+ sss_grad=sscale_grad_martini(dist_sub)
+ LJ1 = (lip_sig(ityp,jtyp)/dist_sub)**6
+ LJ2 = LJ1**2
+ LJ = LJ2 - LJ1
+ LJ = 4.0d0*lip_eps(ityp,jtyp)*LJ
+ eliplj = eliplj + LJ*sss
+ fac=4.0d0*lip_eps(ityp,jtyp)*(-6.0d0*LJ1/dist_sub+12.0d0*LJ2/dist_sub)
+ do k=1,3
+ gradliplj(k,i)=gradliplj(k,i)+fac*dist(k)/dist_sub*sss-sss_grad*LJ*dist(k)/dist_sub
+ gradliplj(k,j)=gradliplj(k,j)-fac*dist(k)/dist_sub*sss+sss_grad*LJ*dist(k)/dist_sub
+ enddo
- if (energy_dec) write(iout,*) "LJ LIP",i,j,ityp,jtyp,LJ,dist_sub
++ if (energy_dec) write(iout,'(a7,4i5,2f8.3)') "LJ LIP",i,j,ityp,jtyp,LJ,dist_sub
+ enddo
+ return
+ end subroutine lipid_lj
+!--------------------------------------------------------------------------------------
+ subroutine lipid_elec(elipelec)
+ real(kind=8) :: elipelec,fac,sumdist,dist_sub,xj,yj,zj,xi,yi,zi,EQ,&
+ sss,sss_grad
+ real(kind=8), dimension(3):: dist
+ integer :: i,j,k,inum,ityp,jtyp
+ elipelec=0.0d0
+! print *,"processor",fg_rank,ilip_elec_start,ilipelec_end
+ do inum=ilip_elec_start,ilipelec_end
+ i=mlipeleclisti(inum)
+ j=mlipeleclistj(inum)
+! print *,inum,i,j,"processor",fg_rank
+ ityp=itype(i,4)
+ jtyp=itype(j,4)
+ xi=c(1,i)
+ yi=c(2,i)
+ zi=c(3,i)
+ call to_box(xi,yi,zi)
+ xj=c(1,j)
+ yj=c(2,j)
+ zj=c(3,j)
+ call to_box(xj,yj,zj)
+ xj=boxshift(xj-xi,boxxsize)
+ yj=boxshift(yj-yi,boxysize)
+ zj=boxshift(zj-zi,boxzsize)
+ dist(1)=xj
+ dist(2)=yj
+ dist(3)=zj
+! do k=1,3
+! dist(k)=c(k,j)-c(k,i)
+! enddo
+ sumdist=0.0d0
+ do k=1,3
+ sumdist=sumdist+dist(k)**2
+ enddo
+ dist_sub=sqrt(sumdist)
+ sss=sscale_martini(dist_sub)
+! print *,sss,dist_sub
+ if (energy_dec) write(iout,*) "EQ LIP",sss,dist_sub,i,j
+ if (sss.le.0.0) cycle
+ sss_grad=sscale_grad_martini(dist_sub)
+! print *,"sss",sss,sss_grad
+ EQ=k_coulomb_lip*(ichargelipid(ityp)*ichargelipid(jtyp)/dist_sub)
+ elipelec=elipelec+EQ*sss
+ fac=k_coulomb_lip*(ichargelipid(ityp)*ichargelipid(jtyp)/sumdist)*sss
+ do k=1,3
+ gradlipelec(k,i)=gradlipelec(k,i)+fac*dist(k)/dist_sub&
+ -sss_grad*EQ*dist(k)/dist_sub
+ gradlipelec(k,j)=gradlipelec(k,j)-fac*dist(k)/dist_sub&
+ +sss_grad*EQ*dist(k)/dist_sub
+ enddo
+ if (energy_dec) write(iout,*) "EQ LIP",i,j,ityp,jtyp,EQ,dist_sub,elipelec
+ enddo
+ return
+ end subroutine lipid_elec
+!-------------------------------------------------------------------------
+ subroutine make_SCSC_inter_list
+ include 'mpif.h'
+ real(kind=8) :: xi,yi,zi,xj,yj,zj,xj_safe,yj_safe,zj_safe,xj_temp,yj_temp,zj_temp
+ real(kind=8) :: dist_init, dist_temp,r_buff_list
+ integer:: contlisti(250*nres),contlistj(250*nres)
+! integer :: newcontlisti(200*nres),newcontlistj(200*nres)
+ integer i,j,itypi,itypj,subchap,xshift,yshift,zshift,iint,ilist_sc,g_ilist_sc
+ integer displ(0:nprocs),i_ilist_sc(0:nprocs),ierr
+! print *,"START make_SC"
+ r_buff_list=5.0
+ ilist_sc=0
+ do i=iatsc_s,iatsc_e
+ itypi=iabs(itype(i,1))
+ if (itypi.eq.ntyp1) cycle
+ xi=c(1,nres+i)
+ yi=c(2,nres+i)
+ zi=c(3,nres+i)
+ call to_box(xi,yi,zi)
+ do iint=1,nint_gr(i)
+! print *,"is it wrong", iint,i
+ do j=istart(i,iint),iend(i,iint)
+ itypj=iabs(itype(j,1))
+ if (energy_dec) write(iout,*) "LISTA ZAKRES",istart(i,iint),iend(i,iint),iatsc_s,iatsc_e
+ if (itypj.eq.ntyp1) cycle
+ xj=c(1,nres+j)
+ yj=c(2,nres+j)
+ zj=c(3,nres+j)
+ call to_box(xj,yj,zj)
+! call lipid_layer(xj,yj,zj,sslipj,ssgradlipj)
+! faclipij2=(sslipi+sslipj)/2.0d0*lipscale**2+1.0d0
xj=boxshift(xj-xi,boxxsize)
yj=boxshift(yj-yi,boxysize)
zj=boxshift(zj-zi,boxzsize)
#endif
return
end subroutine lipid_layer
+!-------------------------------------------------------------
+ subroutine ecat_prot_transition(ecation_prottran)
+ integer:: itypi,itypj,ityptrani,ityptranj,k,l,i,j
+ real(kind=8),dimension(3):: cjtemp,citemp,diff,dsctemp,vecsc,&
+ diffnorm,boxx,r,dEvan1Cm,dEvan2Cm,dEtotalCm
+ real(kind=8):: ecation_prottran,dista,sdist,De,ene,x0left,&
+ alphac,grad,sumvec,simplesum,pom,erdxi,facd1,&
+ sss_ele_cut,sss_ele_cut_grad,sss2min,sss2mingrad,&
+ ene1,ene2,grad1,grad2,evan1,evan2,rcal,r4,r7,r0p,&
+ r06,r012,epscalc,rocal,ract
+ ecation_prottran=0.0d0
+ boxx(1)=boxxsize
+ boxx(2)=boxysize
+ boxx(3)=boxzsize
+ do k=g_listcatsctran_start,g_listcatsctran_end
+ i=newcontlistcatsctrani(k)
+ j=newcontlistcatsctranj(k)
+! print *,i,j,"in new tran"
+ do l=1,3
+ citemp(l)=c(l,i+nres)
+ cjtemp(l)=c(l,j)
+ enddo
+
+ itypi=itype(i,1) !as the first is the protein part
+ itypj=itype(j,5) !as the second part is always cation
+! remapping to internal types
+! read (iiontran,*,err=123,end=123) (agamacattran(k,j,i),k=1,3),&
+! (athetacattran(k,j,i),k=1,6),acatshiftdsc(j,i),bcatshiftdsc(j,i),&
+! demorsecat(j,i),alphamorsecat(j,i),x0catleft(j,i),x0catright(j,i),&
+! x0cattrans(j,i)
+
+ if (itypj.eq.6) then
+ ityptranj=1 !as now only Zn2+ is this needs to be modified for other ions
+ endif
+ if (itypi.eq.16) then
+ ityptrani=1
+ elseif (itypi.eq.1) then
+ ityptrani=2
+ elseif (itypi.eq.15) then
+ ityptrani=3
+ elseif (itypi.eq.17) then
+ ityptrani=4
+ elseif (itypi.eq.2) then
+ ityptrani=5
+ else
+ ityptrani=6
+ endif
+
+ if (ityptrani.gt.ntrantyp(ityptranj)) then
+! do l=1,3
+! write(iout,*),gradcattranc(l,j),gradcattranx(l,i)
+! enddo
+!volume excluded
+ call to_box(cjtemp(1),cjtemp(2),cjtemp(3))
+ call to_box(citemp(1),citemp(2),citemp(3))
+ rcal=0.0d0
+ do l=1,3
+ r(l)=boxshift(cjtemp(l)-citemp(l),boxx(l))
+ rcal=rcal+r(l)*r(l)
+ enddo
+ ract=sqrt(rcal)
+ if (ract.gt.r_cut_ele) cycle
+ sss_ele_cut=sscale_ele(ract)
+ sss_ele_cut_grad=sscagrad_ele(ract)
+ rocal=1.5
+ epscalc=0.2
+ r0p=0.5*(rocal+sig0(itype(i,1)))
+ r06 = r0p**6
+ r012 = r06*r06
+ Evan1=epscalc*(r012/rcal**6)
+ Evan2=epscalc*2*(r06/rcal**3)
+ r4 = rcal**4
+ r7 = rcal**7
+ do l=1,3
+ dEvan1Cm(l) = 12*r(l)*epscalc*r012/r7
+ dEvan2Cm(l) = 12*r(l)*epscalc*r06/r4
+ enddo
+ do l=1,3
+ dEtotalCm(l)=(dEvan1Cm(l)+dEvan2Cm(l))*sss_ele_cut-&
+ (Evan1+Evan2)*sss_ele_cut_grad*r(l)/ract
+ enddo
+ ecation_prottran = ecation_prottran+&
+ (Evan1+Evan2)*sss_ele_cut
+ do l=1,3
+ gradcattranx(l,i)=gradcattranx(l,i)+dEtotalCm(l)
+ gradcattranc(l,i)=gradcattranc(l,i)+dEtotalCm(l)
+ gradcattranc(l,j)=gradcattranc(l,j)-dEtotalCm(l)
+ enddo
+
+ ene=0.0d0
+ else
+! cycle
+ sumvec=0.0d0
+ simplesum=0.0d0
+ do l=1,3
+ vecsc(l)=citemp(l)-c(l,i)
+ sumvec=sumvec+vecsc(l)**2
+ simplesum=simplesum+vecsc(l)
+ enddo
+ sumvec=dsqrt(sumvec)
+ call to_box(cjtemp(1),cjtemp(2),cjtemp(3))
+ call to_box(citemp(1),citemp(2),citemp(3))
+! sumvec=2.0d0
+ do l=1,3
+ dsctemp(l)=c(l,i+nres)&
+ +(acatshiftdsc(ityptrani,ityptranj)-1.0d0)*vecsc(l)&
+ +bcatshiftdsc(ityptrani,ityptranj)*vecsc(l)/sumvec
+ enddo
+ call to_box(dsctemp(1),dsctemp(2),dsctemp(3))
+ sdist=0.0d0
+ do l=1,3
+ diff(l)=boxshift(dsctemp(l)-cjtemp(l),boxx(l))
+ sdist=sdist+diff(l)*diff(l)
+ enddo
+ dista=sqrt(sdist)
+ if (dista.gt.r_cut_ele) cycle
+
+ sss_ele_cut=sscale_ele(dista)
+ sss_ele_cut_grad=sscagrad_ele(dista)
+ sss2min=sscale2(dista,x0cattrans(ityptrani,ityptranj)-0.1d0,0.2d0)
+ De=demorsecat(ityptrani,ityptranj)
+ alphac=alphamorsecat(ityptrani,ityptranj)
+ if (sss2min.eq.1.0d0) then
+! print *,"ityptrani",ityptrani,ityptranj
+ x0left=x0catleft(ityptrani,ityptranj) ! to mn
+ ene=sss_ele_cut*(-De+De*(1.0d0-dexp(-alphac*(dista-x0left)))**2)
+ grad=2.0d0*alphac*De*dexp(-alphac*(dista-x0left))*&
+ (1.0d0-dexp(-alphac*(dista-x0left)))*sss_ele_cut&
+ +ene/sss_ele_cut*sss_ele_cut_grad
+ else if (sss2min.eq.0.0d0) then
+ x0left=x0catright(ityptrani,ityptranj)
+ ene=sss_ele_cut*(-De+De*(1.0d0-dexp(-alphac*(dista-x0left)))**2)
+ grad=2.0d0*alphac*De*dexp(-alphac*(dista-x0left))*&
+ (1.0d0-dexp(-alphac*(dista-x0left)))*sss_ele_cut&
+ +ene/sss_ele_cut*sss_ele_cut_grad
+ else
+ sss2mingrad=sscagrad2(dista,x0cattrans(ityptrani,ityptranj)-0.1d0,0.2d0)
+ x0left=x0catleft(ityptrani,ityptranj)
+ ene1=sss_ele_cut*(-De+De*(1.0d0-dexp(-alphac*(dista-x0left)))**2)
+ grad1=2.0d0*alphac*De*dexp(-alphac*(dista-x0left))*&
+ (1.0d0-dexp(-alphac*(dista-x0left)))*sss_ele_cut&
+ +ene/sss_ele_cut*sss_ele_cut_grad
+ x0left=x0catright(ityptrani,ityptranj)
+ ene2=sss_ele_cut*(-De+De*(1.0d0-dexp(-alphac*(dista-x0left)))**2)
+ grad2=2.0d0*alphac*De*dexp(-alphac*(dista-x0left))*&
+ (1.0d0-dexp(-alphac*(dista-x0left)))*sss_ele_cut&
+ +ene/sss_ele_cut*sss_ele_cut_grad
+ ene=sss2min*ene1+(1.0d0-sss2min)*ene2
+ grad=sss2min*grad1+(1.0d0-sss2min)*grad2+sss2mingrad*(ene1-ene2)
+ endif
+ do l=1,3
+ diffnorm(l)= diff(l)/dista
+ enddo
+ erdxi=scalar(diffnorm(1),dc_norm(1,i+nres))
+ facd1=bcatshiftdsc(ityptrani,ityptranj)/sumvec
+
+ do l=1,3
+! DO k= 1, 3
+! ertail(k) = Rtail_distance(k)/Rtail
+! END DO
+! erdxi = scalar( ertail(1), dC_norm(1,i+nres) )
+! erdxj = scalar( ertail(1), dC_norm(1,j+nres) )
+! facd1 = dtail(1,itypi,itypj) * vbld_inv(i+nres)
+! facd2 = dtail(2,itypi,itypj) * vbld_inv(j+nres)
+! DO k = 1, 3
+!c! write (*,*) "Gvdwc(",k,",",i,")=", gvdwc(k,i)
+!c! write (*,*) "Gvdwc(",k,",",j,")=", gvdwc(k,j)
+! pom = ertail(k)-facd1*(ertail(k)-erdxi*dC_norm(k,i+nres))
+! gvdwx(k,i) = gvdwx(k,i) &
+! - (( dFdR + gg(k) ) * pom)
+ pom=diffnorm(l)+facd1*(diffnorm(l)-erdxi*dc_norm(l,i+nres))
+! write(iout,*),gradcattranc(l,j),gradcattranx(l,i),grad*diff(l)/dista
+
+ gradcattranx(l,i)=gradcattranx(l,i)+grad*pom&
+ +grad*diffnorm(l)*(acatshiftdsc(ityptrani,ityptranj)-1.0d0)
+! *( bcatshiftdsc(ityptrani,ityptranj)*&
+! (1.0d0/sumvec-(vecsc(l)*simplesum)*(sumvec**(-3.0d0))))
+ gradcattranc(l,i)=gradcattranc(l,i)+grad*diff(l)/dista
+! +sss_ele_cut_grad*ene*diff(l)/dista/sss_ele_cut
+ gradcattranc(l,j)=gradcattranc(l,j)-grad*diff(l)/dista
+! -sss_ele_cut_grad*ene*diff(l)/dista/sss_ele_cut
+ enddo
+ ecation_prottran=ecation_prottran+ene
+ if (energy_dec) write(iout,*) "etrancat",i,j,ene,x0left,De,dista,&
+ alphac
+ endif
+ enddo
+! do k=g_listcatptran_start,g_listcatptran_end
+! ene=0.0d0 this will be used if peptide group interaction is needed
+! enddo
+
+
+ return
+ end subroutine
+ subroutine ecat_prot_ang(ecation_protang)
+ integer:: itypi,itypj,ityptrani,ityptranj,k,l,i,j,n,m,&
+ ityptrani1,ityptranj1,ityptrani2,ityptranj2,&
+ i1,i2,j1,j2,k1,k2,k3,i3,j3,ityptrani3,ityptranj3
+
+ real(kind=8),dimension(3):: cjtemp,citemp,diff,dsctemp,vecsc,&
+ diffnorm,boxx,dscvec,dscvecnorm,diffnorm2,&
+ dscvec2,dscvecnorm2,cjtemp2,citemp2,diff2,dsctemp2,&
+ vecsc2,diff1,diffnorm1,diff3,mindiffnorm2
+ real(kind=8),dimension(3):: dscvec1,dscvecnorm1,cjtemp1,citemp1,vecsc1,dsctemp1,&
+ dscvec3,dscvecnorm3,cjtemp3,citemp3,vecsc3,dsctemp3,&
+ diffnorm3,diff4,diffnorm4
+
+ real(kind=8):: ecation_protang,dista,sdist,De,ene,x0left,&
+ alphac,grad,sumvec,sumdscvec,pom,erdxi,facd1,&
+ sss_ele_cut,sss_ele_cut_grad,sss2min,sss2mingrad,&
+ simplesum,cosval,part1,part2a,part2,part2b,part3,&
+ part4a,part4b,part4,bottom,dista2,sdist2,sumvec2,&
+ sumdscvec2,simplesum2,dista1,sdist1,sumvec1,simplesum1,&
+ sumdscvec1,facd2,scal1a,scal1b,scal2a,scal2b,&
+ sss2mingrad1,sss2mingrad2,sss2min1,sss2min2,pom1,pom2,&
+ det1ij,det2ij,cosom1,cosom2,cosom12,cosphij,dista3,&
+ sumvec3
+ real(kind=8):: sinom1,sinom2,sinaux,dephiij,sumdscvec3,sumscvec3,&
+ cosphi,sdist3,simplesum3,det1t2ij,sss2mingrad3,sss2min3,&
+ scal1c,scal2c,scal3a,scal3b,scal3c,facd3,facd2b,scal3d,&
+ scal3e,dista4,sdist4,pom3,sssmintot
+
+ ecation_protang=0.0d0
+ boxx(1)=boxxsize
+ boxx(2)=boxysize
+ boxx(3)=boxzsize
+! print *,"KUR**3",g_listcatscang_start,g_listcatscang_end
+! go to 19
+! go to 21
+ do k=g_listcatscang_start,g_listcatscang_end
+ ene=0.0d0
+ i=newcontlistcatscangi(k)
+ j=newcontlistcatscangj(k)
+ itypi=itype(i,1) !as the first is the protein part
+ itypj=itype(j,5) !as the second part is always cation
+! print *,"KUR**4",i,j,itypi,itypj
+! remapping to internal types
+! read (iiontran,*,err=123,end=123) (agamacattran(k,j,i),k=1,3),&
+! (athetacattran(k,j,i),k=1,6),acatshiftdsc(j,i),bcatshiftdsc(j,i),&
+! demorsecat(j,i),alphamorsecat(j,i),x0catleft(j,i),x0catright(j,i),&
+! x0cattrans(j,i)
+ if (itypj.eq.6) then
+ ityptranj=1 !as now only Zn2+ is this needs to be modified for other ions
+ endif
+ if (itypi.eq.16) then
+ ityptrani=1
+ elseif (itypi.eq.1) then
+ ityptrani=2
+ elseif (itypi.eq.15) then
+ ityptrani=3
+ elseif (itypi.eq.17) then
+ ityptrani=4
+ elseif (itypi.eq.2) then
+ ityptrani=5
+ else
+ ityptrani=6
+ endif
+ if (ityptrani.gt.ntrantyp(ityptranj)) cycle
+ do l=1,3
+ citemp(l)=c(l,i+nres)
+ cjtemp(l)=c(l,j)
+ enddo
+ sumvec=0.0d0
+ simplesum=0.0d0
+ do l=1,3
+ vecsc(l)=citemp(l)-c(l,i)
+ sumvec=sumvec+vecsc(l)**2
+ simplesum=simplesum+vecsc(l)
+ enddo
+ sumvec=dsqrt(sumvec)
+ sumdscvec=0.0d0
+ do l=1,3
+ dsctemp(l)=c(l,i)&
+! +1.0d0
+ +(acatshiftdsc(ityptrani,ityptranj))*vecsc(l)&
+ +bcatshiftdsc(ityptrani,ityptranj)*vecsc(l)/sumvec
+ dscvec(l)= &
+!1.0d0
+ (acatshiftdsc(ityptrani,ityptranj))*vecsc(l)&
+ +bcatshiftdsc(ityptrani,ityptranj)*vecsc(l)/sumvec
+ sumdscvec=sumdscvec+dscvec(l)**2
+ enddo
+ sumdscvec=dsqrt(sumdscvec)
+ do l=1,3
+ dscvecnorm(l)=dscvec(l)/sumdscvec
+ enddo
+ call to_box(dsctemp(1),dsctemp(2),dsctemp(3))
+ call to_box(cjtemp(1),cjtemp(2),cjtemp(3))
+ sdist=0.0d0
+ do l=1,3
+ diff(l)=boxshift(dsctemp(l)-cjtemp(l),boxx(l))
+ sdist=sdist+diff(l)*diff(l)
+ enddo
+ dista=sqrt(sdist)
+ do l=1,3
+ diffnorm(l)= diff(l)/dista
+ enddo
+ cosval=scalar(diffnorm(1),dc_norm(1,i+nres))
+ grad=0.0d0
+ sss2min=sscale2(dista,r_cut_ang,1.0d0)
+ sss2mingrad=sscagrad2(dista,r_cut_ang,1.0d0)
+ ene=ene&
+ +tschebyshev(1,6,athetacattran(1,ityptrani,ityptranj),cosval)
+ grad=gradtschebyshev(0,5,athetacattran(1,ityptrani,ityptranj),cosval)*sss2min
+
+ facd1=bcatshiftdsc(ityptrani,ityptranj)/sumvec
+ erdxi=scalar(diffnorm(1),dc_norm(1,i+nres))
+ part1=0.0d0
+ part2=0.0d0
+ part3=0.0d0
+ part4=0.0d0
+ do l=1,3
+ bottom=sumvec**2*sdist
+ part1=diff(l)*sumvec*dista
+ part2a=(acatshiftdsc(ityptrani,ityptranj))*vecsc(l)
+ part2b=0.0d0
+ !bcatshiftdsc(ityptrani,ityptranj)/sumvec*&
+ !(vecsc(l)-cosval*dista*dc_norm(l,i+nres))
+ part2=(part2a+part2b)*sumvec*dista
+ part3=cosval*sumvec*dista*dc_norm(l,i+nres)*dista
+ part4a=diff(l)*acatshiftdsc(ityptrani,ityptranj)
+ part4b=bcatshiftdsc(ityptrani,ityptranj)/sumvec*&
+ (diff(l)-cosval*dista*dc_norm(l,i+nres))
+ part4=cosval*sumvec*(part4a+part4b)*sumvec
+! gradlipang(m,l)=gradlipang(m,l)+(fac &
+! *(xa(m)-scalar*vnorm*xb(m)/wnorm)&
+! /(vnorm*wnorm))
+
+! DO k= 1, 3
+! ertail(k) = Rtail_distance(k)/Rtail
+! END DO
+! erdxi = scalar( ertail(1), dC_norm(1,i+nres) )
+! erdxj = scalar( ertail(1), dC_norm(1,j+nres) )
+! facd1 = dtail(1,itypi,itypj) * vbld_inv(i+nres)
+! facd2 = dtail(2,itypi,itypj) * vbld_inv(j+nres)
+! DO k = 1, 3
+!c! write (*,*) "Gvdwc(",k,",",i,")=", gvdwc(k,i)
+!c! write (*,*) "Gvdwc(",k,",",j,")=", gvdwc(k,j)
+! pom = ertail(k)-facd1*(ertail(k)-erdxi*dC_norm(k,i+nres))
+! gvdwx(k,i) = gvdwx(k,i) &
+! - (( dFdR + gg(k) ) * pom)
+ pom=diffnorm(l)+facd1*(diffnorm(l)-erdxi*dc_norm(l,i+nres))
+
+ gradcatangc(l,j)=gradcatangc(l,j)-grad*&
+ (dscvec(l)-cosval*diffnorm(l)*sumdscvec)/(sumdscvec*dista)-&
+ ene*sss2mingrad*diffnorm(l)
+
+ gradcatangc(l,i)=gradcatangc(l,i)+grad*&
+ (dscvec(l)-cosval*diffnorm(l)*sumdscvec)/(sumdscvec*dista)+&
+ ene*sss2mingrad*diffnorm(l)
+
+ gradcatangx(l,i)=gradcatangx(l,i)+grad*&
+ (part1+part2-part3-part4)/bottom+&
+ ene*sss2mingrad*pom+&
+ ene*sss2mingrad*diffnorm(l)*(acatshiftdsc(ityptrani,ityptranj)-1.0d0)
+! +grad*(dscvec(l)-cosval*diffnorm(l)*sumdscvec)/(sumdscvec*dista)&
+! +grad*pom+grad*diffnorm(l)*(acatshiftdsc(ityptrani,ityptranj)-1.0d0)
+!&
+! (diff(l)-cosval*dscvecnorm(l)*dista)/(sumdscvec*dista)
+
+
+
+
+
+ enddo
+! print *,i,j,cosval,tschebyshev(1,3,aomicattr(1,ityptranj),cosval)&
+! ,aomicattr(0,ityptranj),ene
+ if (energy_dec) write(iout,*) i,j,ityptrani,ityptranj,ene,cosval
+ ecation_protang=ecation_protang+ene*sss2min
+ enddo
+ 19 continue
+! print *,"KUR**",g_listcatscangf_start,g_listcatscangf_end
+ do k=g_listcatscangf_start,g_listcatscangf_end
+ ene=0.0d0
+ i1=newcontlistcatscangfi(k)
+ j1=newcontlistcatscangfj(k)
+ itypi=itype(i1,1) !as the first is the protein part
+ itypj=itype(j1,5) !as the second part is always cation
+ if (itypj.eq.6) then
+ ityptranj1=1 !as now only Zn2+ is this needs to be modified for other ions
+ endif
+ if (itypi.eq.16) then
+ ityptrani1=1
+ elseif (itypi.eq.1) then
+ ityptrani1=2
+ elseif (itypi.eq.15) then
+ ityptrani1=3
+ elseif (itypi.eq.17) then
+ ityptrani1=4
+ elseif (itypi.eq.2) then
+ ityptrani1=5
+ else
+ ityptrani1=6
+ endif
+ do l=1,3
+ citemp1(l)=c(l,i1+nres)
+ cjtemp1(l)=c(l,j1)
+ enddo
+ sumvec1=0.0d0
+ simplesum1=0.0d0
+ do l=1,3
+ vecsc1(l)=citemp1(l)-c(l,i1)
+ sumvec1=sumvec1+vecsc1(l)**2
+ simplesum1=simplesum1+vecsc1(l)
+ enddo
+ sumvec1=dsqrt(sumvec1)
+ sumdscvec1=0.0d0
+ do l=1,3
+ dsctemp1(l)=c(l,i1)&
+! +1.0d0
+ +(acatshiftdsc(ityptrani1,ityptranj1))*vecsc1(l)&
+ +bcatshiftdsc(ityptrani1,ityptranj1)*vecsc1(l)/sumvec1
+ dscvec1(l)= &
+!1.0d0
+ (acatshiftdsc(ityptrani1,ityptranj1))*vecsc1(l)&
+ +bcatshiftdsc(ityptrani1,ityptranj1)*vecsc1(l)/sumvec1
+ sumdscvec1=sumdscvec1+dscvec1(l)**2
+ enddo
+ sumdscvec1=dsqrt(sumdscvec1)
+ do l=1,3
+ dscvecnorm1(l)=dscvec1(l)/sumdscvec1
+ enddo
+ call to_box(dsctemp1(1),dsctemp1(2),dsctemp1(3))
+ call to_box(cjtemp1(1),cjtemp1(2),cjtemp1(3))
+ sdist1=0.0d0
+ do l=1,3
+ diff1(l)=boxshift(dsctemp1(l)-cjtemp1(l),boxx(l))
+ sdist1=sdist1+diff1(l)*diff1(l)
+ enddo
+ dista1=sqrt(sdist1)
+ do l=1,3
+ diffnorm1(l)= diff1(l)/dista1
+ enddo
+ sss2min1=sscale2(dista1,r_cut_ang,1.0d0)
+ sss2mingrad1=sscagrad2(dista1,r_cut_ang,1.0d0)
+ if (ityptrani1.gt.ntrantyp(ityptranj1)) cycle
+
+!-----------------------------------------------------------------
+! do m=k+1,g_listcatscang_end
+ ene=0.0d0
+ i2=newcontlistcatscangfk(k)
+ j2=j1
+ if (j1.ne.j2) cycle
+ itypi=itype(i2,1) !as the first is the protein part
+ itypj=itype(j2,5) !as the second part is always cation
+ if (itypj.eq.6) then
+ ityptranj2=1 !as now only Zn2+ is this needs to be modified for other ions
+ endif
+ if (itypi.eq.16) then
+ ityptrani2=1
+ elseif (itypi.eq.1) then
+ ityptrani2=2
+ elseif (itypi.eq.15) then
+ ityptrani2=3
+ elseif (itypi.eq.17) then
+ ityptrani2=4
+ elseif (itypi.eq.2) then
+ ityptrani2=5
+ else
+ ityptrani2=6
+ endif
+ if (ityptrani2.gt.ntrantyp(ityptranj2)) cycle
+
+ do l=1,3
+ citemp2(l)=c(l,i2+nres)
+ cjtemp2(l)=c(l,j2)
+ enddo
+ sumvec2=0.0d0
+ simplesum2=0.0d0
+ do l=1,3
+ vecsc2(l)=citemp2(l)-c(l,i2)
+ sumvec2=sumvec2+vecsc2(l)**2
+ simplesum2=simplesum2+vecsc2(l)
+ enddo
+ sumvec2=dsqrt(sumvec2)
+ sumdscvec2=0.0d0
+ do l=1,3
+ dsctemp2(l)=c(l,i2)&
+! +1.0d0
+ +(acatshiftdsc(ityptrani2,ityptranj2))*vecsc2(l)&
+ +bcatshiftdsc(ityptrani2,ityptranj2)*vecsc2(l)/sumvec2
+ dscvec2(l)= &
+!1.0d0
+ (acatshiftdsc(ityptrani2,ityptranj2))*vecsc2(l)&
+ +bcatshiftdsc(ityptrani2,ityptranj2)*vecsc2(l)/sumvec2
+ sumdscvec2=sumdscvec2+dscvec2(l)**2
+ enddo
+ sumdscvec2=dsqrt(sumdscvec2)
+ do l=1,3
+ dscvecnorm2(l)=dscvec2(l)/sumdscvec2
+ enddo
+ call to_box(dsctemp2(1),dsctemp2(2),dsctemp2(3))
+ call to_box(cjtemp2(1),cjtemp2(2),cjtemp2(3))
+ sdist2=0.0d0
+ do l=1,3
+ diff2(l)=boxshift(dsctemp2(l)-cjtemp2(l),boxx(l))
+! diff2(l)=1.0d0
+ sdist2=sdist2+diff2(l)*diff2(l)
+ enddo
+ dista2=sqrt(sdist2)
+ do l=1,3
+ diffnorm2(l)= diff2(l)/dista2
+ enddo
+! print *,i1,i2,diffnorm2(1)
+ cosval=scalar(diffnorm1(1),diffnorm2(1))
+ grad=0.0d0
+ sss2min2=sscale2(dista2,r_cut_ang,1.0d0)
+ sss2mingrad2=sscagrad2(dista2,r_cut_ang,1.0d0)
+ ene=ene+tschebyshev(1,3,aomicattr(1,ityptranj1),cosval)
+ grad=gradtschebyshev(0,2,aomicattr(1,ityptranj1),cosval)*sss2min2*sss2min1
+ part1=0.0d0
+ part2=0.0d0
+ part3=0.0d0
+ part4=0.0d0
+ ecation_protang=ecation_protang+ene*sss2min2*sss2min1
+ facd1=bcatshiftdsc(ityptrani1,ityptranj1)/sumvec1
+ facd2=bcatshiftdsc(ityptrani2,ityptranj2)/sumvec2
+ scal1a=scalar(diffnorm1(1),dc_norm(1,i1+nres))
+ scal1b=scalar(diffnorm2(1),dc_norm(1,i1+nres))
+ scal2a=scalar(diffnorm1(1),dc_norm(1,i2+nres))
+ scal2b=scalar(diffnorm2(1),dc_norm(1,i2+nres))
+
+ if (energy_dec) write(iout,*) "omi", i,j,ityptrani,ityptranj,ene,cosval,aomicattr(1,ityptranj1),&
+ aomicattr(2,ityptranj1),aomicattr(3,ityptranj1),tschebyshev(1,3,aomicattr(1,ityptranj1),cosval)
+
+!*sss2min
+ do l=1,3
+ pom1=diffnorm1(l)+facd1*(diffnorm1(l)-scal1a*dc_norm(l,i1+nres))
+ pom2=diffnorm2(l)+facd2*(diffnorm2(l)-scal2b*dc_norm(l,i2+nres))
+
+
+ gradcatangc(l,i1)=gradcatangc(l,i1)+grad*(diff2(l)-&
+ cosval*diffnorm1(l)*dista2)/(dista2*dista1)+&
+ ene*sss2mingrad1*diffnorm1(l)*sss2min2
+
+
+ gradcatangx(l,i1)=gradcatangx(l,i1)+grad/(dista2*dista1)*&
+ (acatshiftdsc(ityptrani1,ityptranj1)*diff2(l)+&
+ facd1*(diff2(l)-scal1b*dc_norm(l,i1+nres)*dista2)-&
+ cosval*dista2/dista1*&
+ (acatshiftdsc(ityptrani1,ityptranj1)*diff1(l)+&
+ facd1*(diff1(l)-scal1a*dc_norm(l,i1+nres)*dista1)))+&
+ ene*sss2mingrad1*sss2min2*(pom1+&
+ diffnorm1(l)*(acatshiftdsc(ityptrani1,ityptranj1)-1.0d0))
+
+
+ gradcatangx(l,i2)=gradcatangx(l,i2)+grad/(dista2*dista1)*&
+ (acatshiftdsc(ityptrani2,ityptranj2)*diff1(l)+&
+ facd2*(diff1(l)-scal2a*dc_norm(l,i2+nres)*dista1)-&
+ cosval*dista1/dista2*&
+ (acatshiftdsc(ityptrani2,ityptranj2)*diff2(l)+&
+ facd2*(diff2(l)-scal2b*dc_norm(l,i2+nres)*dista2)))+&
+ ene*sss2mingrad2*sss2min1*(pom2+&
+ diffnorm2(l)*(acatshiftdsc(ityptrani2,ityptranj2)-1.0d0))
+
+
+ gradcatangx(l,i2)=gradcatangx(l,i2)
+ gradcatangc(l,i2)=gradcatangc(l,i2)+grad*(diff1(l)-&
+ cosval*diffnorm2(l)*dista1)/(dista2*dista1)+&
+ ene*sss2mingrad2*diffnorm2(l)*sss2min1
+
+ gradcatangc(l,j2)=gradcatangc(l,j2)-grad*(diff2(l)/dista2/dista1-&
+ cosval*diff1(l)/dista1/dista1+diff1(l)/dista2/dista1-&
+ cosval*diff2(l)/dista2/dista2)-&
+ ene*sss2mingrad1*diffnorm1(l)*sss2min2-&
+ ene*sss2mingrad2*diffnorm2(l)*sss2min1
+
+
+ enddo
+
+ enddo
+! enddo
+!#ifdef DUBUG
+ 21 continue
+! do k1=g_listcatscang_start,g_listcatscang_end
+! print *,"KURNA",g_listcatscangt_start,g_listcatscangt_end
+ do k1=g_listcatscangt_start,g_listcatscangt_end
+ i1=newcontlistcatscangti(k1)
+ j1=newcontlistcatscangtj(k1)
+ itypi=itype(i1,1) !as the first is the protein part
+ itypj=itype(j1,5) !as the second part is always cation
+ if (itypj.eq.6) then
+ ityptranj1=1 !as now only Zn2+ is this needs to be modified for other ions
+ endif
+ if (itypi.eq.16) then
+ ityptrani1=1
+ elseif (itypi.eq.1) then
+ ityptrani1=2
+ elseif (itypi.eq.15) then
+ ityptrani1=3
+ elseif (itypi.eq.17) then
+ ityptrani1=4
+ elseif (itypi.eq.2) then
+ ityptrani1=5
+ else
+ ityptrani1=6
+ endif
+ do l=1,3
+ citemp1(l)=c(l,i1+nres)
+ cjtemp1(l)=c(l,j1)
+ enddo
+ sumvec1=0.0d0
+ simplesum1=0.0d0
+ do l=1,3
+ vecsc1(l)=citemp1(l)-c(l,i1)
+ sumvec1=sumvec1+vecsc1(l)**2
+ simplesum1=simplesum1+vecsc1(l)
+ enddo
+ sumvec1=dsqrt(sumvec1)
+ sumdscvec1=0.0d0
+ do l=1,3
+ dsctemp1(l)=c(l,i1)&
+ +(acatshiftdsc(ityptrani1,ityptranj1))*vecsc1(l)&
+ +bcatshiftdsc(ityptrani1,ityptranj1)*vecsc1(l)/sumvec1
+ dscvec1(l)= &
+ (acatshiftdsc(ityptrani1,ityptranj1))*vecsc1(l)&
+ +bcatshiftdsc(ityptrani1,ityptranj1)*vecsc1(l)/sumvec1
+ sumdscvec1=sumdscvec1+dscvec1(l)**2
+ enddo
+ sumdscvec1=dsqrt(sumdscvec1)
+ do l=1,3
+ dscvecnorm1(l)=dscvec1(l)/sumdscvec1
+ enddo
+ call to_box(dsctemp1(1),dsctemp1(2),dsctemp1(3))
+ call to_box(cjtemp1(1),cjtemp1(2),cjtemp1(3))
+ sdist1=0.0d0
+ do l=1,3
+ diff1(l)=boxshift(dsctemp1(l)-cjtemp1(l),boxx(l))
+ sdist1=sdist1+diff1(l)*diff1(l)
+ enddo
+ dista1=sqrt(sdist1)
+ do l=1,3
+ diffnorm1(l)= diff1(l)/dista1
+ enddo
+ sss2min1=sscale2(dista1,r_cut_ang,1.0d0)
+ sss2mingrad1=sscagrad2(dista1,r_cut_ang,1.0d0)
+ if (ityptrani1.gt.ntrantyp(ityptranj1)) cycle
+!---------------before second loop
+! do k2=k1+1,g_listcatscang_end
+ i2=newcontlistcatscangtk(k1)
+ j2=j1
+! print *,"TUTU3",i1,i2,j1,j2
+ if (i2.eq.i1) cycle
+ if (j2.ne.j1) cycle
+ itypi=itype(i2,1) !as the first is the protein part
+ itypj=itype(j2,5) !as the second part is always cation
+ if (itypj.eq.6) then
+ ityptranj2=1 !as now only Zn2+ is this needs to be modified for other ions
+ endif
+ if (itypi.eq.16) then
+ ityptrani2=1
+ elseif (itypi.eq.1) then
+ ityptrani2=2
+ elseif (itypi.eq.15) then
+ ityptrani2=3
+ elseif (itypi.eq.17) then
+ ityptrani2=4
+ elseif (itypi.eq.2) then
+ ityptrani2=5
+ else
+ ityptrani2=6
+ endif
+ if (ityptrani2.gt.ntrantyp(ityptranj2)) cycle
+ do l=1,3
+ citemp2(l)=c(l,i2+nres)
+ cjtemp2(l)=c(l,j2)
+ enddo
+ sumvec2=0.0d0
+ simplesum2=0.0d0
+ do l=1,3
+ vecsc2(l)=citemp2(l)-c(l,i2)
+ sumvec2=sumvec2+vecsc2(l)**2
+ simplesum2=simplesum2+vecsc2(l)
+ enddo
+ sumvec2=dsqrt(sumvec2)
+ sumdscvec2=0.0d0
+ do l=1,3
+ dsctemp2(l)=c(l,i2)&
+ +(acatshiftdsc(ityptrani2,ityptranj2))*vecsc2(l)&
+ +bcatshiftdsc(ityptrani2,ityptranj2)*vecsc2(l)/sumvec2
+ dscvec2(l)= &
+ (acatshiftdsc(ityptrani2,ityptranj2))*vecsc2(l)&
+ +bcatshiftdsc(ityptrani2,ityptranj2)*vecsc2(l)/sumvec2
+ sumdscvec2=sumdscvec2+dscvec2(l)**2
+ enddo
+ sumdscvec2=dsqrt(sumdscvec2)
+ do l=1,3
+ dscvecnorm2(l)=dscvec2(l)/sumdscvec2
+ enddo
+ call to_box(dsctemp2(1),dsctemp2(2),dsctemp2(3))
+ call to_box(cjtemp2(1),cjtemp2(2),cjtemp2(3))
+ sdist2=0.0d0
+ do l=1,3
+ diff2(l)=boxshift(dsctemp2(l)-cjtemp2(l),boxx(l))
+! diff2(l)=1.0d0
+ sdist2=sdist2+diff2(l)*diff2(l)
+ enddo
+ dista2=sqrt(sdist2)
+ do l=1,3
+ diffnorm2(l)= diff2(l)/dista2
+ mindiffnorm2(l)=-diffnorm2(l)
+ enddo
+! print *,i1,i2,diffnorm2(1)
+ cosom1=scalar(diffnorm1(1),diffnorm2(1))
+ sss2min2=sscale2(dista2,r_cut_ang,1.0d0)
+ sss2mingrad2=sscagrad2(dista2,r_cut_ang,1.0d0)
+
+!---------------- before third loop
+! do k3=g_listcatscang_start,g_listcatscang_end
+ ene=0.0d0
+ i3=newcontlistcatscangtl(k1)
+ j3=j1
+! print *,"TUTU4",i1,i2,i3,j1,j2,j3
+
+ if (i3.eq.i2) cycle
+ if (i3.eq.i1) cycle
+ if (j3.ne.j1) cycle
+ itypi=itype(i3,1) !as the first is the protein part
+ itypj=itype(j3,5) !as the second part is always cation
+ if (itypj.eq.6) then
+ ityptranj3=1 !as now only Zn2+ is this needs to be modified for other ions
+ endif
+ if (itypi.eq.16) then
+ ityptrani3=1
+ elseif (itypi.eq.1) then
+ ityptrani3=2
+ elseif (itypi.eq.15) then
+ ityptrani3=3
+ elseif (itypi.eq.17) then
+ ityptrani3=4
+ elseif (itypi.eq.2) then
+ ityptrani3=5
+ else
+ ityptrani3=6
+ endif
+ if (ityptrani3.gt.ntrantyp(ityptranj3)) cycle
+ do l=1,3
+ citemp3(l)=c(l,i3+nres)
+ cjtemp3(l)=c(l,j3)
+ enddo
+ sumvec3=0.0d0
+ simplesum3=0.0d0
+ do l=1,3
+ vecsc3(l)=citemp3(l)-c(l,i3)
+ sumvec3=sumvec3+vecsc3(l)**2
+ simplesum3=simplesum3+vecsc3(l)
+ enddo
+ sumvec3=dsqrt(sumvec3)
+ sumdscvec3=0.0d0
+ do l=1,3
+ dsctemp3(l)=c(l,i3)&
+ +(acatshiftdsc(ityptrani3,ityptranj3))*vecsc3(l)&
+ +bcatshiftdsc(ityptrani3,ityptranj3)*vecsc3(l)/sumvec3
+ dscvec3(l)= &
+ (acatshiftdsc(ityptrani3,ityptranj3))*vecsc3(l)&
+ +bcatshiftdsc(ityptrani3,ityptranj3)*vecsc3(l)/sumvec3
+ sumdscvec3=sumdscvec3+dscvec3(l)**2
+ enddo
+ sumdscvec3=dsqrt(sumdscvec3)
+ do l=1,3
+ dscvecnorm3(l)=dscvec3(l)/sumdscvec3
+ enddo
+ call to_box(dsctemp3(1),dsctemp3(2),dsctemp3(3))
+ call to_box(cjtemp3(1),cjtemp3(2),cjtemp3(3))
+ sdist3=0.0d0
+ do l=1,3
+ diff3(l)=boxshift(dsctemp3(l)-dsctemp2(l),boxx(l))
+ sdist3=sdist3+diff3(l)*diff3(l)
+ enddo
+ dista3=sqrt(sdist3)
+ do l=1,3
+ diffnorm3(l)= diff3(l)/dista3
+ enddo
+ sdist4=0.0d0
+ do l=1,3
+ diff4(l)=boxshift(dsctemp3(l)-cjtemp2(l),boxx(l))
+! diff2(l)=1.0d0
+ sdist4=sdist4+diff4(l)*diff4(l)
+ enddo
+ dista4=sqrt(sdist4)
+ do l=1,3
+ diffnorm4(l)= diff4(l)/dista4
+ enddo
+
+ sss2min3=sscale2(dista4,r_cut_ang,1.0d0)
+ sss2mingrad3=sscagrad2(dista4,r_cut_ang,1.0d0)
+ sssmintot=sss2min3*sss2min2*sss2min1
+ if (ityptrani3.gt.ntrantyp(ityptranj3)) cycle
+ cosom12=scalar(diffnorm3(1),diffnorm1(1))
+ cosom2=scalar(diffnorm3(1),mindiffnorm2(1))
+ sinom1=dsqrt(1.0d0-cosom1*cosom1)
+ sinom2=dsqrt(1.0d0-cosom2*cosom2)
+ cosphi=cosom12-cosom1*cosom2
+ sinaux=sinom1*sinom2
+ ene=ene+mytschebyshev(1,3,agamacattran(1,ityptrani2,ityptranj2),cosphi,sinaux)
+ call mygradtschebyshev(1,3,agamacattran(1,ityptrani2,ityptranj2)&
+ ,cosphi,sinaux,dephiij,det1t2ij)
+
+ det1ij=-det1t2ij*sinom2*cosom1/sinom1-dephiij*cosom2
+ det2ij=-det1t2ij*sinom1*cosom2/sinom2-dephiij*cosom1
+ facd1=bcatshiftdsc(ityptrani1,ityptranj1)/sumvec1
+ facd2=bcatshiftdsc(ityptrani2,ityptranj2)/sumvec2
+! facd2b=bcatshiftdsc(ityptrani2,ityptranj2)/sumvec3
+ facd3=bcatshiftdsc(ityptrani3,ityptranj3)/sumvec3
+ scal1a=scalar(diffnorm1(1),dc_norm(1,i1+nres))
+ scal1b=scalar(diffnorm2(1),dc_norm(1,i1+nres))
+ scal1c=scalar(diffnorm3(1),dc_norm(1,i1+nres))
+ scal2a=scalar(diffnorm1(1),dc_norm(1,i2+nres))
+ scal2b=scalar(diffnorm2(1),dc_norm(1,i2+nres))
+ scal2c=scalar(diffnorm3(1),dc_norm(1,i2+nres))
+ scal3a=scalar(diffnorm1(1),dc_norm(1,i3+nres))
+ scal3b=scalar(mindiffnorm2(1),dc_norm(1,i3+nres))
+ scal3d=scalar(diffnorm2(1),dc_norm(1,i3+nres))
+ scal3c=scalar(diffnorm3(1),dc_norm(1,i3+nres))
+ scal3e=scalar(diffnorm4(1),dc_norm(1,i3+nres))
+
+ do l=1,3
+ pom1=diffnorm1(l)+facd1*(diffnorm1(l)-scal1a*dc_norm(l,i1+nres))
+ pom2=diffnorm2(l)+facd2*(diffnorm2(l)-scal2b*dc_norm(l,i2+nres))
+ pom3=diffnorm4(l)+facd3*(diffnorm4(l)-scal3e*dc_norm(l,i3+nres))
+
+ gradcatangc(l,i1)=gradcatangc(l,i1)&
+ +det1ij*sssmintot*(diff2(l)-diffnorm1(l)*cosom1*dista2)/(dista2*dista1)+&
+ dephiij*sssmintot*(diff3(l)-diffnorm1(l)*cosom12*dista3)/(dista3*dista1)&
+ +ene*sss2mingrad1*diffnorm1(l)*sss2min2*sss2min3
+
+
+ gradcatangc(l,i2)=gradcatangc(l,i2)+(&
+ det1ij*(diff1(l)-diffnorm2(l)*cosom1*dista1)/(dista2*dista1)+&
+ det2ij*(-diff3(l)+mindiffnorm2(l)*cosom2*dista3)/(dista3*dista2)&
+ -det2ij*(-diff2(l)-diffnorm3(l)*cosom2*dista2)/(dista3*dista2)&
+ -dephiij*(diff1(l)-diffnorm3(l)*cosom12*dista1)/(dista3*dista1))*sssmintot&
+ +ene*sss2mingrad2*diffnorm2(l)*sss2min1*sss2min3
+
+
+
+ gradcatangc(l,i3)=gradcatangc(l,i3)&
+ +det2ij*(-diff2(l)-diffnorm3(l)*cosom2*dista2)/(dista3*dista2)*sssmintot&
+ +dephiij*(diff1(l)-diffnorm3(l)*cosom12*dista1)/(dista3*dista1)*sssmintot&
+ +ene*sss2mingrad3*diffnorm4(l)*sss2min1*sss2min2
+
+
+ gradcatangc(l,j1)=gradcatangc(l,j1)-&
+ sssmintot*(det1ij*(diff2(l)-diffnorm1(l)*cosom1*dista2)/(dista2*dista1)+&
+ dephiij*(diff3(l)-diffnorm1(l)*cosom12*dista3)/(dista3*dista1))&
+ -(det1ij*(diff1(l)-diffnorm2(l)*cosom1*dista1)/(dista1*dista2)+&
+ det2ij*(-diff3(l)+mindiffnorm2(l)*cosom2*dista3)/(dista3*dista2))*sssmintot&
+ -ene*sss2mingrad1*diffnorm1(l)*sss2min2*sss2min3&
+ -ene*sss2mingrad2*diffnorm2(l)*sss2min1*sss2min3&
+ -ene*sss2mingrad3*diffnorm4(l)*sss2min1*sss2min2
+
+
+ gradcatangx(l,i1)=gradcatangx(l,i1)+(det1ij/(dista2*dista1)*&
+ (acatshiftdsc(ityptrani1,ityptranj1)*diff2(l)+&
+ facd1*(diff2(l)-scal1b*dc_norm(l,i1+nres)*dista2)-&
+ cosom1*dista2/dista1*&
+ (acatshiftdsc(ityptrani1,ityptranj1)*diff1(l)+&
+ facd1*(diff1(l)-scal1a*dc_norm(l,i1+nres)*dista1)))&
+ +dephiij/(dista3*dista1)*&
+ (acatshiftdsc(ityptrani1,ityptranj1)*diff3(l)+&
+ facd1*(diff3(l)-scal1c*dc_norm(l,i1+nres)*dista3)-&
+ cosom12*dista3/dista1*&
+ (acatshiftdsc(ityptrani1,ityptranj1)*diff1(l)+&
+ facd1*(diff1(l)-scal1a*dc_norm(l,i1+nres)*dista1))))*sssmintot&
+ +ene*sss2mingrad1*sss2min2*sss2min3*(pom1+&
+ diffnorm1(l)*(acatshiftdsc(ityptrani1,ityptranj1)-1.0d0))
+
+
+ gradcatangx(l,i3)=gradcatangx(l,i3)+(&
+ det2ij/(dista3*dista2)*&
+ (acatshiftdsc(ityptrani3,ityptranj3)*(-diff2(l))+&
+ facd3*(-diff2(l)-scal3b*dc_norm(l,i3+nres)*dista2)-&
+ cosom2*dista2/dista3*&
+ (acatshiftdsc(ityptrani3,ityptranj3)*diff3(l)+&
+ facd3*(diff3(l)-scal3c*dc_norm(l,i3+nres)*dista3)))&
+ +dephiij/(dista3*dista1)*&
+ (acatshiftdsc(ityptrani3,ityptranj3)*diff1(l)+&
+ facd3*(diff1(l)-scal3a*dc_norm(l,i3+nres)*dista1)-&
+ cosom12*dista1/dista3*&
+ (acatshiftdsc(ityptrani3,ityptranj3)*diff3(l)+&
+ facd3*(diff3(l)-scal3c*dc_norm(l,i3+nres)*dista3))))*sssmintot&
+ +ene*sss2mingrad3*sss2min2*sss2min1*(pom3+&
+ diffnorm4(l)*(acatshiftdsc(ityptrani3,ityptranj3)-1.0d0))
+
+
+ gradcatangx(l,i2)=gradcatangx(l,i2)+(&!
+ det1ij/(dista2*dista1)*&!
+ (acatshiftdsc(ityptrani2,ityptranj2)*diff1(l)&!
+ +facd2*(diff1(l)-scal2a*dc_norm(l,i2+nres)*dista1)&
+ -cosom1*dista1/dista2*&!
+ (acatshiftdsc(ityptrani2,ityptranj2)*diff2(l)+&!
+ facd2*(diff2(l)-scal2b*dc_norm(l,i2+nres)*dista2)))+&
+ det2ij/(dista3*dista2)*&!
+ (acatshiftdsc(ityptrani2,ityptranj2)*diff2(l)+&!
+ facd2*(diff2(l)-scal2b*dc_norm(l,i2+nres)*dista2)&
+ -(acatshiftdsc(ityptrani2,ityptranj2)*diff3(l)+&!
+ facd2*(diff3(l)-scal2c*dc_norm(l,i2+nres)*dista3))&
+ -cosom2*dista3/dista2*&!
+ (acatshiftdsc(ityptrani2,ityptranj2)*diff2(l)+&!
+ facd2*(diff2(l)-scal2b*dc_norm(l,i2+nres)*dista2))&
+ +cosom2*dista2/dista3*&!
+ (acatshiftdsc(ityptrani2,ityptranj2)*diff3(l)+&!
+ facd2*(diff3(l)-scal2c*dc_norm(l,i2+nres)*dista3)))&
+ +dephiij/(dista3*dista1)*&!
+ (-(acatshiftdsc(ityptrani2,ityptranj2)*diff1(l)+&!
+ facd2*(diff1(l)-scal2a*dc_norm(l,i2+nres)*dista1))+&
+ cosom12*dista1/dista3*&!
+ (acatshiftdsc(ityptrani2,ityptranj2)*diff3(l)+&!
+ facd2*(diff3(l)-scal2c*dc_norm(l,i2+nres)*dista3))))*sssmintot&
+ +ene*sss2mingrad2*sss2min3*sss2min1*(pom2+&
+ diffnorm2(l)*(acatshiftdsc(ityptrani2,ityptranj2)-1.0d0))
+
+
+ enddo
+! print *,i1,i2,i3,j1,j2,j3,"tors",ene,sinaux,cosphi
+! print *,"param",agamacattran(1,ityptrani2,ityptranj2),ityptranj2,ityptrani2
+ ecation_protang=ecation_protang+ene*sssmintot
+ enddo
+! enddo
+! enddo
+!#endif
+ return
+ end subroutine
!--------------------------------------------------------------------------
+!c------------------------------------------------------------------------------
+ double precision function mytschebyshev(m,n,x,y,yt)
+ implicit none
+ integer i,m,n
+ double precision x(n),y,yt,yy(0:100),aux
+!c Tschebyshev polynomial in y multiplied by sin(t1)sin(t2) (yt).
+!c Note that the first term is omitted
+!c m=0: the constant term is included
+!c m=1: the constant term is not included
+ yy(0)=1.0d0
+ yy(1)=y
+ do i=2,n
+ yy(i)=2*yy(1)*yy(i-1)-yy(i-2)*yt*yt
+ enddo
+ aux=0.0d0
+ do i=m,n
+ aux=aux+x(i)*yy(i)
+ enddo
+!c print *,(yy(i),i=1,n)
+ mytschebyshev=aux
+ return
+ end function
+!C--------------------------------------------------------------------------
+!C--------------------------------------------------------------------------
+ subroutine mygradtschebyshev(m,n,x,y,yt,fy,fyt)
+ implicit none
+ integer i,m,n
+ double precision x(n+1),y,yt,fy,fyt,yy(0:100),yb(0:100), &
+ ybt(0:100)
+!c Derivative of Tschebyshev polynomial in y multiplied by sin(t1)sin(t2) (yt).
+!c Note that the first term is omitted
+!c m=0: the constant term is included
+!c m=1: the constant term is not included
+ yy(0)=1.0d0
+ yy(1)=y
+ yb(0)=0.0d0
+ yb(1)=1.0d0
+ ybt(0)=0.0d0
+ ybt(1)=0.0d0
+ do i=2,n
+ yy(i)=2*yy(1)*yy(i-1)-yy(i-2)*yt*yt
+ yb(i)=2*yy(i-1)+2*yy(1)*yb(i-1)-yb(i-2)*yt*yt
+ ybt(i)=2*yy(1)*ybt(i-1)-ybt(i-2)*yt*yt-2*yy(i-2)*yt
+ enddo
+ fy=0.0d0
+ fyt=0.0d0
+ do i=m,n
+ fy=fy+x(i)*yb(i)
+ fyt=fyt+x(i)*ybt(i)
+ enddo
+ return
+ end subroutine
++ subroutine fodstep(nsteps)
++ use geometry_data, only: c, nres, theta, alph
++ use geometry, only:alpha,beta,dist
++ integer, intent(in) :: nsteps
++ integer idxtomod, j, i
++ double precision RD0, RD1, fi
++! double precision alpha
++! double precision beta
++! double precision dist
++! double precision compute_RD
++ double precision TT
++ real :: r21(5)
++!c ! Założenia: dla łańcucha zapisanego w tablicy c zawierającego
++!c ! nres elementów CA i CB da się wyznaczyć kąty płaskie
++!c ! theta (procedura Alpha) i kąty torsyjne (procedura beta),
++!c ! zapisywane w tablicach theta i alph.
++!c ! Na podstawie danych z tych tablic da się odtworzyć
++!c ! strukturę 3D łańcucha procedurą chainbuild.
++!c !
++! print *,"fodstep: nres=",nres
++ RD0 = compute_RD()
++! print *, "RD0before step: ",RD0
++ do j=1,nsteps
++!c ! Wyznaczenie kątów theta na podstawie struktury
++!c ! zapisanej w tablicy c
++ do i=3,nres
++ TT=alpha(i-2,i-1,i)
++ theta(i)=TT
++!c print *,"TT=",TT
++ end do
++!c ! Wyznaczenie kątów phi na podstawie struktury
++!c ! zapisanej w tablicy c
++ do i=4,nres
++ phi(i)=beta(i-3,i-2,i-1,i)
++ end do
++!c ! Wyznaczenie odległości między atomami
++!c ! vbld(i)=dist(i-1,i)
++ do i=2,nres
++ vbld(i)=dist(i-1,i)
++ end do
++!c ! losujemy kilka liczb
++ call random_number(r21)
++!c ! r21(1): indeks pozycji do zmiany
++!c ! r21(2): kąt (r21(2)/20.0-1/40.0)
++!c ! r21(3): wybór tablicy
++ RD0 = compute_RD()
++!c print *, "RD before step: ",RD0
++ fi = (r21(2)/20.0-1.0/40.0) ! o tyle radianów zmienimy losowy kąt
++ if (r21(3) .le. 0.5) then
++ idxtomod = 3+r21(1)*(nres - 2)
++ theta(idxtomod) = theta(idxtomod)+fi
++! print *,"Zmiana kąta theta(",&
++! idxtomod,") o fi = ",fi
++ else
++ idxtomod = 4+r21(1)*(nres - 3)
++ phi(idxtomod) = phi(idxtomod)+fi
++! print *,"Zmiana kąta phi(",&
++! idxtomod,") o fi = ",fi
++ end if
++!c ! odtwarzamy łańcuch
++ call chainbuild
++!c ! czy coś się polepszyło?
++ RD1 = compute_RD()
++ if (RD1 .gt. RD0) then ! nie, wycofujemy zmianę
++! print *, "RD after step: ",RD1," rejected"
++ if (r21(3) .le. 0.5) then
++ theta(idxtomod) = theta(idxtomod)-fi
++ else
++ phi(idxtomod) = phi(idxtomod)-fi
++ end if
++ call chainbuild ! odtworzenie pierwotnej wersji (bez zmienionego kąta)
++ else
++! print *, "RD after step: ",RD1," accepted"
++ continue
++ end if
++ end do
++ end subroutine
++!c-----------------------------------------------------------------------------------------
++ subroutine orientation_matrix(res) ! obliczenie macierzy oraz przygotowanie ea z tymi przeksztalceniami
++ use geometry_data, only: c, nres
++ use energy_data, only: itype
++ double precision, intent(out) :: res(4,4)
++ double precision resM(4,4)
++ double precision M(4,4)
++ double precision M2(4,4)
++ integer i, j, maxi, maxj
++! double precision sq
++ double precision maxd, dd
++ double precision v1(3)
++ double precision v2(3)
++ double precision vecnea(3)
++ double precision mean_ea(3)
++ double precision fi
++!c ! liczymy atomy efektywne i zapisujemy w tablicy ea
++ do i=1,nres
++!c if (itype(i,1) .ne. 10) then
++ if (itype(i,1) .ne. 10) then
++ ea(1,i) = c(1,i+nres)
++ ea(2,i) = c(2,i+nres)
++ ea(3,i) = c(3,i+nres)
++ else
++ ea(1,i) = c(1,i)
++ ea(2,i) = c(2,i)
++ ea(3,i) = c(3,i)
++ end if
++ end do
++ call IdentityM(resM)
++ if (nres .le. 2) then
++ print *, "nres too small (should be at least 2), stopping"
++ stop
++ end if
++ do i=1,3
++ v1(i)=ea(i,1)
++ v2(i)=ea(i,2)
++ end do
++!c ! szukamy najwiekszej odleglosci miedzy atomami efektywnymi ea
++ call Dist3d(maxd,v1,v2)
++!c ! odleglosc miedzy pierwsza para atomow efektywnych
++ maxi = 1
++ maxj = 2
++ do i=1,nres-1
++ do j=i+1,nres
++ v1(1)=ea(1,i)
++ v1(2)=ea(2,i)
++ v1(3)=ea(3,i)
++ v2(1)=ea(1,j)
++ v2(2)=ea(2,j)
++ v2(3)=ea(3,j)
++ call Dist3d(dd,v1,v2)
++ if (dd .gt. maxd) then
++ maxd = dd
++ maxi = i
++ maxj = j
++ end if
++ end do
++ end do
++ vecnea(1)=ea(1,maxi)-ea(1,maxj)
++ vecnea(2)=ea(2,maxi)-ea(2,maxj)
++ vecnea(3)=ea(3,maxi)-ea(3,maxj)
++ if (vecnea(1) .lt. 0) then
++ vecnea(1) = -vecnea(1)
++ vecnea(2) = -vecnea(2)
++ vecnea(3) = -vecnea(3)
++ end if
++!c ! obliczenie kata obrotu wokol osi Z
++ fi = -atan2(vecnea(2),vecnea(1))
++ call RotateZ(M,fi)
++!c ! obliczenie kata obrotu wokol osi Y
++ fi = atan2(vecnea(3), sqrt(sq(vecnea(1))+sq(vecnea(2))))
++ call RotateY(M2,fi)
++ M = matmul(M2,M)
++!c ! Przeksztalcamy wszystkie atomy efektywne
++!c ! uzyskujac najwieksza odleglosc ulożona wzdluz OX
++!c ! ea = transform_eatoms(ea,M)
++ do i=1,nres
++ v1(1)=ea(1,i)
++ v1(2)=ea(2,i)
++ v1(3)=ea(3,i)
++ call tranform_point(v2,v1,M)
++ ea(1,i)=v2(1)
++ ea(2,i)=v2(2)
++ ea(3,i)=v2(3)
++ end do
++ resM = M
++!c ! Teraz szukamy najdluzszego rzutu na plaszczyzne YZ
++!c ! (czyli w liczeniu odleglosci bierzemy pod uwage tylko wsp. y, z)
++ maxd = sqrt( sq(ea(2,1)-ea(2,2)) + sq(ea(3,1)-ea(3,2))) ! aktualnie max odl
++ maxi = 1 ! indeksy atomow
++ maxj = 2 ! miedzy ktorymi jest max odl (chwilowe)
++ do i=1,nres-1
++ do j=i+1,nres
++ dd = sqrt( (ea(2,i)-ea(2,j))**2 + (ea(3,i)-ea(3,j))**2)
++ if (dd .gt. maxd) then
++ maxd = dd
++ maxi = i
++ maxj = j
++ end if
++ end do
++ end do
++!c ! Teraz obrocimy wszystko wokol OX tak, zeby znaleziony rzut
++!c ! byl rownolegly do OY
++ vecnea(1) = ea(1,maxi)-ea(1,maxj)
++ vecnea(2) = ea(2,maxi)-ea(2,maxj)
++ vecnea(3) = ea(3,maxi)-ea(3,maxj)
++!c ! jeśli współrzędna vecnea.y < 0, to robimy odwrotnie
++ if (vecnea(2) .lt. 0) then
++ vecnea(1) = -vecnea(1)
++ vecnea(2) = -vecnea(2)
++ vecnea(3) = -vecnea(3)
++ end if
++!c ! obliczenie kąta obrotu wokół osi X
++ fi = -atan2(vecnea(3),vecnea(2))
++ call RotateX(M,fi)
++!c ! Przeksztalcamy wszystkie atomy efektywne
++ do i=1,nres
++ v1(1)=ea(1,i)
++ v1(2)=ea(2,i)
++ v1(3)=ea(3,i)
++ call tranform_point(v2,v1,M)
++ ea(1,i)=v2(1)
++ ea(2,i)=v2(2)
++ ea(3,i)=v2(3)
++ end do
++ resM = matmul(M,resM) ! zbieramy wynik (sprawdzic kolejnosc M,resM)
++!c ! centrujemy
++ mean_ea(1) = 0
++ mean_ea(2) = 0
++ mean_ea(3) = 0
++ do i=1,nres
++ mean_ea(1) = mean_ea(1) + ea(1,i)
++ mean_ea(2) = mean_ea(2) + ea(2,i)
++ mean_ea(3) = mean_ea(3) + ea(3,i)
++ end do
++ v1(1) = -mean_ea(1)/nres
++ v1(2) = -mean_ea(2)/nres
++ v1(3) = -mean_ea(3)/nres
++ call TranslateV(M,v1)
++ resM = matmul(M,resM)
++!c ! przesuwamy
++ do i=1,nres
++ ea(1,i) = ea(1,i) + v1(1)
++ ea(2,i) = ea(2,i) + v1(2)
++ ea(3,i) = ea(3,i) + v1(3)
++ end do
++ res = resM
++!c ! wynikowa macierz przeksztalcenia lancucha
++!c ! (ale lancuch w ea juz mamy przeksztalcony)
++ return
++ end subroutine
++ double precision function compute_rd
++ use geometry_data, only: nres
++ use energy_data, only: itype
++ implicit none
++ double precision or_mat(4,4)
++! double precision hydrophobicity
++ integer neatoms
++ double precision cutoff
++ double precision ho(70000)
++ double precision ht(70000)
++ double precision hosum, htsum
++ double precision marg, sigmax, sigmay, sigmaz
++ integer i, j
++ double precision v1(3)
++ double precision v2(3)
++ double precision rijdivc, coll, tmpkwadrat, tmppotega, dist
++ double precision OdivT, OdivR, ot_one, or_one, RD_classic
++ call orientation_matrix(or_mat)
++!c ! tam juz liczy sie tablica ea
++ neatoms = nres
++ cutoff = 8.99d0
++!c ! granica oddzialywania w A (powyzej ignorujemy oddzialywanie)
++!c ! Najpierw liczymy "obserwowana hydrofobowosc"
++ hosum = 0.0d0 ! na sume pol ho, do celow pozniejszej normalizacji
++ do j=1,neatoms
++ ho(j)=0.0d0
++ do i=1,neatoms
++ if (j .eq. i) then ! nie uwzgledniamy oddzialywania atomu z samym soba
++ cycle
++ end if
++ v1(1)=ea(1,i)
++ v1(2)=ea(2,i)
++ v1(3)=ea(3,i)
++ v2(1)=ea(1,j)
++ v2(2)=ea(2,j)
++ v2(3)=ea(3,j)
++ call Dist3d(dist,v1,v2) ! odleglosc miedzy atomami
++ if (dist .gt. cutoff) then ! za daleko, nie uwzgledniamy
++ cycle
++ end if
++ rijdivc = dist / cutoff
++ coll = 0.0d0
++ tmppotega = rijdivc*rijdivc
++ tmpkwadrat = tmppotega
++ coll = coll + 7*tmpkwadrat
++ tmppotega = tmppotega * tmpkwadrat ! do potęgi 4
++ coll = coll - 9*tmppotega
++ tmppotega = tmppotega * tmpkwadrat ! do potęgi 6
++ coll = coll + 5*tmppotega
++ tmppotega = tmppotega * tmpkwadrat ! do potęgi 8
++ coll = coll - tmppotega
++!c ! Wersja: Bryliński 2007
++!c ! EAtoms[j].collectedhp += EAtoms[i].hyphob*(1 - 0.5 * coll);
++!c ! ea$ho[j] = ea$ho[j] + hydrophobicity(ea$resid[i])*(1-0.5*coll)
++!c ! Wersja: Banach Konieczny Roterman 2014
++!c ! EAtoms[j].collectedhp += (EAtoms[i].hyphob+EAtoms[j].hyphob)*(1 - 0.5 * coll);
++!c ponizej bylo itype(i,1) w miejscu itype(i) oraz itype(j,1) w miejscu itype(j)
++ ho(j) = ho(j) + (hydrophobicity(itype(i,1))+&
++ hydrophobicity(itype(j,1)))*(1.0d0-0.5_8*coll)
++ end do
++ hosum = hosum + ho(j)
++ end do
++!c ! Normalizujemy
++ do i=1,neatoms
++ ho(i) = ho(i) / hosum
++ end do
++!c ! Koniec liczenia hydrofobowosci obserwowanej (profil ho)
++!c ! Teraz liczymy "teoretyczna hydrofobowosc", wedlug kropli i rozkladu Gaussa
++ htsum = 0.0d0
++!c ! tu zbieramy sume ht, uzyjemy potem do normalizacji
++!c ! Ustalimy teraz parametry rozkladu Gaussa, czyli sigmy (srodek jest w (0,0,0)).
++!c ! To bedzie (max odl od srodka + margines) / 3, oddzielnie dla kazdej wspolrzednej.
++ marg = 9.0d0
++ htsum = 0.0d0
++!c ! jeszcze raz zerujemy
++!c ! szukamy ekstremalnej wartosci wspolrzednej x (max wart bezwzgl)
++ sigmax = ea(1,1)
++ do i=2,neatoms
++ if (abs(ea(1,i))>sigmax) then
++ sigmax = abs(ea(1,i))
++ end if
++ end do
++ sigmax = (marg + sigmax) / 3.0d0
++!c ! szukamy ekstremalnej wartosci wspolrzednej y (max wart bezwzgl)
++ sigmay = ea(2,1)
++ do i=2,neatoms
++ if (abs(ea(2,i))>sigmay) then
++ sigmay = abs(ea(2,i))
++ end if
++ end do
++ sigmay = (marg + sigmay) / 3.0d0
++!c ! szukamy ekstremalnej wartosci wspolrzednej z (max wart bezwzgl)
++ sigmaz = ea(3,1)
++ do i=2,neatoms
++ if (abs(ea(3,i))>sigmaz) then
++ sigmaz = abs(ea(3,i))
++ end if
++ end do
++ sigmaz = (marg + sigmaz) / 3.0d0
++!c !sigmax = (marg + max(abs(max(ea$acoor[,1])), abs(min(ea$acoor[,1]))))/3.0
++!c !sigmay = (marg + max(abs(max(ea$acoor[,2])), abs(min(ea$acoor[,2]))))/3.0
++!c !sigmaz = (marg + max(abs(max(ea$acoor[,3])), abs(min(ea$acoor[,3]))))/3.0
++!c ! print *,"sigmax =",sigmax," sigmay =",sigmay," sigmaz = ",sigmaz
++ do j=1,neatoms
++ ht(j)= exp(-(ea(1,j))**2/(2*sigmax**2))&
++ * exp(-(ea(2,j))**2/(2*sigmay**2)) &
++ * exp(-(ea(3,j))**2/(2*sigmaz**2))
++ htsum = htsum + ht(j)
++ end do
++!c ! Normalizujemy
++ do i=1, neatoms
++ ht(i) = ht(i) / htsum
++ end do
++!c ! Teraz liczymy RD
++ OdivT = 0.0d0
++ OdivR = 0.0d0
++ do j=1,neatoms
++ if (ho(j) .ne. 0) then
++ ot_one = ho(j) * log(ho(j)/ht(j)) / log(2.0d0)
++ OdivT = OdivT + ot_one
++ or_one = ho(j) * log(ho(j)/ (1.0d0/neatoms)) / log(2.0_8)
++ OdivR = OdivR + or_one
++ endif
++ end do
++ RD_classic = OdivT / (OdivT+OdivR)
++ compute_rd = RD_classic
++ return
++ end function
++ function hydrophobicity(id) ! do przepisania (bylo: identyfikowanie aa po nazwach)
++ integer id
++ double precision hydrophobicity
++ hydrophobicity = 0.0d0
++ if (id .eq. 1) then
++ hydrophobicity = 1.000d0 ! CYS
++ return
++ endif
++ if (id .eq. 2) then
++ hydrophobicity = 0.828d0 ! MET
++ return
++ endif
++ if (id .eq. 3) then
++ hydrophobicity = 0.906d0 ! PHE
++ return
++ endif
++ if (id .eq. 4) then
++ hydrophobicity = 0.883d0 ! ILE
++ return
++ endif
++ if (id .eq. 5) then
++ hydrophobicity = 0.783d0 ! LEU
++ return
++ endif
++ if (id .eq. 6) then
++ hydrophobicity = 0.811d0 ! VAL
++ return
++ endif
++ if (id .eq. 7) then
++ hydrophobicity = 0.856d0 ! TRP
++ return
++ endif
++ if (id .eq. 8) then
++ hydrophobicity = 0.700d0 ! TYR
++ return
++ endif
++ if (id .eq. 9) then
++ hydrophobicity = 0.572d0 ! ALA
++ return
++ endif
++ if (id .eq. 10) then
++ hydrophobicity = 0.550d0 ! GLY
++ return
++ endif
++ if (id .eq. 11) then
++ hydrophobicity = 0.478d0 ! THR
++ return
++ endif
++ if (id .eq. 12) then
++ hydrophobicity = 0.422d0 ! SER
++ return
++ endif
++ if (id .eq. 13) then
++ hydrophobicity = 0.250d0 ! GLN
++ return
++ endif
++ if (id .eq. 14) then
++ hydrophobicity = 0.278d0 ! ASN
++ return
++ endif
++ if (id .eq. 15) then
++ hydrophobicity = 0.083d0 ! GLU
++ return
++ endif
++ if (id .eq. 16) then
++ hydrophobicity = 0.167d0 ! ASP
++ return
++ endif
++ if (id .eq. 17) then
++ hydrophobicity = 0.628d0 ! HIS
++ return
++ endif
++ if (id .eq. 18) then
++ hydrophobicity = 0.272d0 ! ARG
++ return
++ endif
++ if (id .eq. 19) then
++ hydrophobicity = 0.000d0 ! LYS
++ return
++ endif
++ if (id .eq. 20) then
++ hydrophobicity = 0.300d0 ! PRO
++ return
++ endif
++ return
++ end function hydrophobicity
++ subroutine mycrossprod(res,b,c)
++ implicit none
++ double precision, intent(out) :: res(3)
++ double precision, intent(in) :: b(3)
++ double precision, intent(in) :: c(3)
++!c ! Tylko dla wektorów trójwymiarowych, ale nie sprawdzamy tego tutaj
++ res(1) = b(2)*c(3)-b(3)*c(2)
++ res(2) = b(3)*c(1)-b(1)*c(3)
++ res(3) = b(1)*c(2)-b(2)*c(1)
++ return
++ end subroutine
++ subroutine mydotprod(res,b,c)
++ implicit none
++ double precision, intent(out) :: res
++ double precision, intent(in) :: b(3)
++ double precision, intent(in) :: c(3)
++!c ! Tylko dla wektorów trójwymiarowych, ale nie sprawdzamy tego tutaj
++ res = b(1)*c(1)+b(2)*c(2)+b(3)*c(3)
++ return
++ end subroutine
++!c ! cosinus k¹ta miêdzy wektorami trójwymiarowymi
++ subroutine cosfi(res, x, y)
++ implicit none
++ double precision, intent(out) :: res
++ double precision, intent(in) :: x(3)
++ double precision, intent(in) :: y(3)
++ double precision LxLy
++ LxLy=sqrt(x(1)*x(1)+x(2)*x(2)+x(3)*x(3)) *&
++ sqrt(y(1)*y(1)+y(2)*y(2)+y(3)*y(3))
++ if (LxLy==0.0) then
++ res = 0.0d0
++ else
++ call mydotprod(res,x,y)
++ res = res / LxLy
++ end if
++ return
++ end subroutine
++
++
++ subroutine Dist3d(res,v1,v2)
++ implicit none
++ double precision, intent(out) :: res
++ double precision, intent(in) :: v1(3)
++ double precision, intent(in) :: v2(3)
++! double precision sq
++ res = sqrt( sq(v1(1)-v2(1)) + sq(v1(2)-v2(2)) + sq(v1(3)-v2(3)))
++ return
++ end subroutine
++!c ! Przeksztalca wsp. 3d uzywajac macierzy przeksztalcenia M (4x4)
++ subroutine tranform_point(res,v3d,M)
++ implicit none
++ double precision, intent(out) :: res(3)
++ double precision, intent(in) :: v3d(3)
++ double precision, intent(in) :: M(4,4)
++
++ res(1) = M(1,1)*v3d(1) + M(1,2)*v3d(2) + M(1,3)*v3d(3) + M(1,4)
++ res(2) = M(2,1)*v3d(1) + M(2,2)*v3d(2) + M(2,3)*v3d(3) + M(2,4)
++ res(3) = M(3,1)*v3d(1) + M(3,2)*v3d(2) + M(3,3)*v3d(3) + M(3,4)
++ return
++ end subroutine
++!c ! TranslateV: macierz translacji o wektor V
++ subroutine TranslateV(res,V)
++ implicit none
++ double precision, intent(out) :: res(4,4)
++ double precision, intent(in) :: v(3)
++ res(1,1) = 1.0d0
++ res(1,2) = 0
++ res(1,3) = 0
++ res(1,4) = v(1)
++ res(2,1) = 0
++ res(2,2) = 1.0d0
++ res(2,3) = 0
++ res(2,4) = v(2)
++ res(3,1) = 0
++ res(3,2) = 0
++ res(3,3) = 1.0d0
++ res(3,4) = v(3)
++ res(4,1) = 0
++ res(4,2) = 0
++ res(4,3) = 0
++ res(4,4) = 1.0d0
++ return
++ end subroutine
++!c ! RotateX: macierz obrotu wokol osi OX o kat fi
++ subroutine RotateX(res,fi)
++ implicit none
++ double precision, intent(out) :: res(4,4)
++ double precision, intent(in) :: fi
++ res(1,1) = 1.0d0
++ res(1,2) = 0
++ res(1,3) = 0
++ res(1,4) = 0
++ res(2,1) = 0
++ res(2,2) = cos(fi)
++ res(2,3) = -sin(fi)
++ res(2,4) = 0
++ res(3,1) = 0
++ res(3,2) = sin(fi)
++ res(3,3) = cos(fi)
++ res(3,4) = 0
++ res(4,1) = 0
++ res(4,2) = 0
++ res(4,3) = 0
++ res(4,4) = 1.0d0
++ return
++ end subroutine
++!c ! RotateY: macierz obrotu wokol osi OY o kat fi
++ subroutine RotateY(res,fi)
++ implicit none
++ double precision, intent(out) :: res(4,4)
++ double precision, intent(in) :: fi
++ res(1,1) = cos(fi)
++ res(1,2) = 0
++ res(1,3) = sin(fi)
++ res(1,4) = 0
++ res(2,1) = 0
++ res(2,2) = 1.0d0
++ res(2,3) = 0
++ res(2,4) = 0
++ res(3,1) = -sin(fi)
++ res(3,2) = 0
++ res(3,3) = cos(fi)
++ res(3,4) = 0
++ res(4,1) = 0
++ res(4,2) = 0
++ res(4,3) = 0
++ res(4,4) = 1.0d0
++ return
++ end subroutine
++!c ! RotateZ: macierz obrotu wokol osi OZ o kat fi
++ subroutine RotateZ(res,fi)
++ implicit none
++ double precision, intent(out) :: res(4,4)
++ double precision, intent(in) :: fi
++ res(1,1) = cos(fi)
++ res(1,2) = -sin(fi)
++ res(1,3) = 0
++ res(1,4) = 0
++ res(2,1) = sin(fi)
++ res(2,2) = cos(fi)
++ res(2,3) = 0
++ res(2,4) = 0
++ res(3,1) = 0
++ res(3,2) = 0
++ res(3,3) = 1.0d0
++ res(3,4) = 0
++ res(4,1) = 0
++ res(4,2) = 0
++ res(4,3) = 0
++ res(4,4) = 1.0d0
++ return
++ end subroutine
++!c ! IdentityM
++ subroutine IdentityM(res)
++ implicit none
++ double precision, intent(out) :: res(4,4)
++ res(1,1) = 1.0d0
++ res(1,2) = 0
++ res(1,3) = 0
++ res(1,4) = 0
++ res(2,1) = 0
++ res(2,2) = 1.0d0
++ res(2,3) = 0
++ res(2,4) = 0
++ res(3,1) = 0
++ res(3,2) = 0
++ res(3,3) = 1.0d0
++ res(3,4) = 0
++ res(4,1) = 0
++ res(4,2) = 0
++ res(4,3) = 0
++ res(4,4) = 1.0d0
++ return
++ end subroutine
++ double precision function sq(x)
++ double precision x
++ sq = x*x
++ return
++ end function sq
+
!--------------------------------------------------------------------------
end module energy
nres2=2*nres
! Set lprn=.true. for debugging
lprn = .false.
-- print *,"I ENTER CHAINBUILD"
++! print *,"I ENTER CHAINBUILD"
!
! Define the origin and orientation of the coordinate system and locate the
! first three CA's and SC(2).
!-----------------------------------------------------------------------------
subroutine returnbox
integer :: allareout,i,j,k,nojumpval,chain_beg,mnum
- integer :: chain_end,ireturnval
- real*8 :: difference
+ integer :: chain_end,ireturnval,idum,mnumi1
+ real*8 :: difference,xi,boxsize,x,xtemp,box2shift
+ real(kind=8),dimension(3) :: boxx
- real(kind=8),dimension(3,100) :: xorg
- integer,dimension(100) :: posdummy
++ real(kind=8),dimension(3,10000) :: xorg
++ integer,dimension(10000) :: posdummy
+
!C change suggested by Ana - end
j=1
chain_beg=1
if (refstr) then
call rms_nac_nnc(rms,frac,frac_nn,co,.false.)
write (line1,'(i10,f15.2,3f12.3,f7.2,2f6.3,4f12.3,i5,$)')&
-- itime,totT,EK,potE,totE,&
++ itime,totT,EK,potE+potEcomp(51),totE+potEcomp(51),&
rms,frac,frac_nn,kinetic_T,t_bath,gyrate(),&
potEcomp(23),me
format1="a133"
else
!C print *,'A CHUJ',potEcomp(23)
write (line1,'(i10,f15.2,7f12.3,i5,$)') &
-- itime,totT,EK,potE,totE,&
++ itime,totT,EK,potE+potEcomp(51),totE+potEcomp(51),&
kinetic_T,t_bath,gyrate(),&
potEcomp(23),me
format1="a114"
call rms_nac_nnc(rms,frac,frac_nn,co,.false.)
write (line1,'(i10,f15.2,3f12.3,f7.2,2f6.3,f12.3,f10.1,2f8.2, &
f9.3,i5,$)') &
-- itime,totT,EK,potE,totE,&
++ itime,totT,EK,potE+potEcomp(51),totE+potEcomp(51),&
rms,frac,frac_nn,kinetic_T,t_bath,gyrate(),&
distance,potEcomp(23),me
format1="a133"
else
!C print *,'A CHUJ',potEcomp(23)
write (line1,'(i10,f15.2,8f12.3,i5,$)')&
-- itime,totT,EK,potE,totE, &
++ itime,totT,EK,potE+potEcomp(51),totE+potEcomp(51), &
kinetic_T,t_bath,gyrate(),&
distance,potEcomp(23),me
format1="a114"
endif
++ else if (velnanoconst.ne.0 ) then
++ if (refstr) then
++ call rms_nac_nnc(rms,frac,frac_nn,co,.false.)
++ write (line1,'(i10,f15.2,3f12.3,f7.2,2f6.3,f12.3,f10.1,2f8.2, &
++ f9.3,i5,$)') &
++ itime,totT,EK,potE+potEcomp(51),totE+potEcomp(51),&
++ rms,frac,frac_nn,kinetic_T,t_bath,gyrate(),&
++ vecsim,vectrue,me
++ format1="a133"
++!C print *,"CHUJOWO"
++ else
++!C print *,'A CHUJ',potEcomp(23)
++ write (line1,'(i10,f15.2,8f12.3,i5,$)')&
++ itime,totT,EK,potE+potEcomp(51),totE+potEcomp(51), &
++ kinetic_T,t_bath,gyrate(),&
++ vecsim,vectrue,me
++ format1="a114"
++ endif
else
if (refstr) then
call rms_nac_nnc(rms,frac,frac_nn,co,.false.)
write (line1,'(i10,f15.2,3f12.3,f7.2,4f6.3,3f12.3,i5,$)') &
-- itime,totT,EK,potE,totE,&
++ itime,totT,EK,potE+potEcomp(51),totE+potEcomp(51),&
rms,frac,frac_nn,co,amax,kinetic_T,t_bath,gyrate(),me
format1="a133"
else
write (line1,'(i10,f15.2,7f12.3,i5,$)') &
-- itime,totT,EK,potE,totE,&
++ itime,totT,EK,potE+potEcomp(51),totE+potEcomp(51),&
amax,kinetic_T,t_bath,gyrate(),me
format1="a114"
endif
vbld(i+nres)=dsc(iabs(itype(i,molnum(i))))
vbld_inv(i+nres)=dsc_inv(iabs(itype(i,molnum(i))))
else
++ write(iout,*) "typy2",itype(i,mnum),ntyp1_molec(mnum),i
++ if (itype(i,mnum).eq.ntyp1_molec(mnum)) then
++ vbld_inv(i+nres)=1.0
++ vbld(i+nres)=0.0
++ else
vbld(i+nres)=vbldsc0_nucl(1,iabs(itype(i,molnum(i))))
vbld_inv(i+nres)=1.0/vbldsc0_nucl(1,iabs(itype(i,molnum(i))))
++ endif
endif
! write (iout,*) "i",i," itype",itype(i,1),
! & " dsc",dsc(itype(i,1))," vbld",vbld(i),vbld(i+nres)
if (constr_dist.gt.0) call read_dist_constr
write (iout,*) "After read_dist_constr nhpb",nhpb
if ((AFMlog.gt.0).or.(selfguide.gt.0)) call read_afminp
++ if (velnanoconst.ne.0) call read_afmnano
call hpb_partition
if (indpdb.eq.0 .and. modecalc.ne.2 .and. modecalc.ne.4 &
use control_data, only:out1file
use MPI_data
character*320 afmcard
-- integer i
++ real, dimension(3) ::cbeg,cend
++ integer i,j
print *, "wchodze"
call card_concat(afmcard,.true.)
call readi(afmcard,"BEG",afmbeg,0)
call reada(afmcard,"FORCE",forceAFMconst,0.0d0)
call reada(afmcard,"VEL",velAFMconst,0.0d0)
print *,'FORCE=' ,forceAFMconst
++ cbeg=0.0d0
++ cend=0.0d0
++ if (afmbeg.eq.-1) then
++ read(inp,*) nbegafmmat,(afmbegcentr(i),i=1,nbegafmmat)
++ do i=1,nbegafmmat
++ do j=1,3
++ cbeg(j)=cbeg(j)+c(j,afmbegcentr(i))/nbegafmmat
++ enddo
++ enddo
++ else
++ do j=1,3
++ cbeg(j)=c(j,afmend)
++ enddo
++ endif
++ if (afmend.eq.-1) then
++ read(inp,*) nendafmmat,(afmendcentr(i),i=1,nendafmmat)
++ do i=1,nendafmmat
++ do j=1,3
++ cend(j)=cend(j)+c(j,afmendcentr(i))/nendafmmat
++ enddo
++ enddo
++ else
++ cend(j)=c(j,afmend)
++ endif
!------ NOW PROPERTIES FOR AFM
distafminit=0.0d0
do i=1,3
-- distafminit=(c(i,afmend)-c(i,afmbeg))**2+distafminit
++ distafminit=(cend(i)-cbeg(i))**2+distafminit
enddo
distafminit=dsqrt(distafminit)
print *,'initdist',distafminit
return
end subroutine read_afminp
++!C------------------------------------------------------------
++ subroutine read_afmnano
++ use geometry_data
++ use energy_data
++ use control_data, only:out1file
++ use MPI_data
++ integer :: i
++ real*8 :: cm
++ read(inp,*,err=11) inanomove,(inanotab(i),i=1,inanomove),forcenanoconst
++ cm=0.0d0
++ do i=1,inanomove
++ cm=cm+c(3,inanotab(i))
++ enddo
++ cm=cm/inanomove
++ distnanoinit=cm-tubecenter(3)
++ return
++11 write(iout,*)&
++ "error in afmnano",&
++ ", number of center, their index and forceconstance"
++ stop
++ return
++ end subroutine read_afmnano
++
!-----------------------------------------------------------------------------
subroutine read_dist_constr
use MPI_data
character(len=640) :: controlcard
!el local variables
-- integer :: i,k,j,ddjk,ii,jj,itemp
++ integer :: i,k,j,ii,jj,itemp,mnumkk,mnumjj,k1,j1
integer :: nfrag_,npair_,ndist_
-- real(kind=8) :: dist_cut
++ real(kind=8) :: dist_cut,ddjk
! write (iout,*) "Calling read_dist_constr"
! write (iout,*) "nres",nres," nstart_sup",nstart_sup," nsup",nsup
call multreadi(controlcard,"IPAIR",ipair_(1,1),2*npair_,0)
call multreada(controlcard,"WFRAG",wfrag_(1),nfrag_,0.0d0)
call multreada(controlcard,"WPAIR",wpair_(1),npair_,0.0d0)
--! write (iout,*) "NFRAG",nfrag_," NPAIR",npair_," NDIST",ndist_
++ write (iout,*) "NFRAG",nfrag_," NPAIR",npair_," NDIST",ndist_
! write (iout,*) "IFRAG"
--! do i=1,nfrag_
--! write (iout,*) i,ifrag_(1,i),ifrag_(2,i),wfrag_(i)
--! enddo
++ do i=1,nfrag_
++ write (iout,*) i,ifrag_(1,i),ifrag_(2,i),wfrag_(i)
++ enddo
! write (iout,*) "IPAIR"
! do i=1,npair_
! write (iout,*) i,ipair_(1,i),ipair_(2,i),wpair_(i)
call flush(iout)
do i=1,nfrag_
-- if (ifrag_(1,i).lt.nstart_sup) ifrag_(1,i)=nstart_sup
-- if (ifrag_(2,i).gt.nstart_sup+nsup-1) &
-- ifrag_(2,i)=nstart_sup+nsup-1
++! if (ifrag_(1,i).lt.nstart_sup) ifrag_(1,i)=nstart_sup
++! if (ifrag_(2,i).gt.nstart_sup+nsup-1) &
++! ifrag_(2,i)=nstart_sup+nsup-1
! write (iout,*) i,ifrag_(1,i),ifrag_(2,i),wfrag_(i)
call flush(iout)
if (wfrag_(i).gt.0.0d0) then
do j=ifrag_(1,i),ifrag_(2,i)-1
do k=j+1,ifrag_(2,i)
--! write (iout,*) "j",j," k",k
++ write (iout,*) "j",j," k",k,nres
++ j1=j
++ k1=k
++ if (j.gt.nres) j1=j-nres
++ if (k.gt.nres) k1=k-nres
++ mnumkk=molnum(k1)
++ mnumjj=molnum(j1)
++
++ if ((itype(k1,mnumkk).gt.ntyp_molec(mnumkk)).or.&
++ (itype(j1,mnumjj).gt.ntyp_molec(mnumjj))) cycle
++ write (iout,*) "j",j," k",k,itype(k1,mnumkk),itype(j1,mnumjj)
ddjk=dist(j,k)
if (constr_dist.eq.1) then
nhpb=nhpb+1
iatom=0
ichain=1
-- ires=0
-- do i=nnt,nct
++ ires=0
++ write(iout,*) "TUTUT"
++ do i=nnt,nct
++ write(iout,*), "coord",c(1,i),c(2,i),c(3,i)
iti=itype(i,molnum(i))
print *,i,molnum(i)
if (molnum(i+1).eq.0) then
if (istype(i).eq.0) istype(i)=1
write (iunit,40) iatom,sugartyp(istype(i)),restyp(iti,2), &
chainid(ichain),ires,(c(j,i),j=1,3),vtot(i)
- else
+ elseif (molnum(i).eq.4) then
+ xi=c(1,i)
+ yi=c(2,i)
+ zi=c(3,i)
- xi=dmod(xi,boxxsize)
- if (xi.lt.0.0d0) xi=xi+boxxsize
- yi=dmod(yi,boxysize)
- if (yi.lt.0.0d0) yi=yi+boxysize
- zi=dmod(zi,boxzsize)
- if (zi.lt.0.0d0) zi=zi+boxzsize
++! xi=dmod(xi,boxxsize)
++! if (xi.lt.0.0d0) xi=xi+boxxsize
++! yi=dmod(yi,boxysize)
++! if (yi.lt.0.0d0) yi=yi+boxysize
++! zi=dmod(zi,boxzsize)
++! if (zi.lt.0.0d0) zi=zi+boxzsize
+ write (iunit,60) iatom,restyp(iti,molnum(i)),chainid(ichain),&
+ ires,xi,yi,zi,vtot(i)
+ else
write (iunit,60) iatom,restyp(iti,molnum(i)),chainid(ichain),&
ires,(c(j,i),j=1,3),vtot(i)
endif
write(iout,*) "Explicit LIPID not yet implemented"
stop
else if (molecule.eq.5) then
-- do i=1,ntyp1_molec(molecule)
++ do i=-1,ntyp1_molec(molecule)
print *,restyp(i,molecule)
print *,i,restyp(i,molecule)(1:2),nam(1:2)
if (ucase(nam(1:2)).eq.restyp(i,molecule)(1:2)) then
dwa16,rjunk,akl,v0ij,rri,epsij,rrij,sigeps,sigt1sq,&
sigt2sq,sigii1,sigii2,ratsig1,ratsig2,rsum_max,r_augm,&
res1,epsijlip,epspeptube,epssctube,sigmapeptube, &
- sigmasctube,krad2
- integer :: ichir1,ichir2,ijunk
- sigmasctube
- integer :: ichir1,ichir2,ijunk
++ sigmasctube,krad2,ract
++ integer :: ichir1,ichir2,ijunk,irdiff
character*3 string
- character*80 temp1
-
++ character*80 temp1,mychar
! real(kind=8),dimension(maxterm,-maxtor:maxtor,-maxtor:maxtor,2) :: v1_el,v2_el !(maxterm,-maxtor:maxtor,-maxtor:maxtor,2)
!el allocate(v1_el(maxterm,-maxtor:maxtor,-maxtor:maxtor,2))
!el allocate(v2_el(maxterm,-maxtor:maxtor,-maxtor:maxtor,2))
msc(:,:)=0.0d0
isc(:,:)=0.0d0
-- allocate(msc(ntyp+1,5)) !(ntyp+1)
-- allocate(isc(ntyp+1,5)) !(ntyp+1)
-- allocate(restok(ntyp+1,5)) !(ntyp+1)
++ allocate(msc(-ntyp-1:ntyp+1,5)) !(ntyp+1)
++ allocate(isc(-ntyp-1:ntyp+1,5)) !(ntyp+1)
++ allocate(restok(-ntyp-1:ntyp+1,5)) !(ntyp+1)
read (ibond,*) junk,vbldp0,vbldpDUM,akp,rjunk,mp(1),ip(1),pstok(1)
do i=1,ntyp_molec(1)
-- if (.not.allocated(ichargecat)) allocate (ichargecat(ntyp_molec(5)))
++ if (.not.allocated(ichargecat)) &
++ allocate (ichargecat(-ntyp_molec(5):ntyp_molec(5)))
++ ichargecat(:)=0
if (oldion.eq.1) then
do i=1,ntyp_molec(5)
read(iion,*) msc(i,5),restok(i,5),ichargecat(i)
print *,liptranene(i)
enddo
close(iliptranpar)
++! water parmaters entalphy
++ allocate(awaterenta(0:400))
++ allocate(bwaterenta(0:400))
++ allocate(cwaterenta(0:400))
++ allocate(dwaterenta(0:400))
++ allocate(awaterentro(0:400))
++ allocate(bwaterentro(0:400))
++ allocate(cwaterentro(0:400))
++ allocate(dwaterentro(0:400))
++
++ read(iwaterwater,*) mychar
++ read(iwaterwater,*) ract,awaterenta(0),bwaterenta(0),&
++ cwaterenta(0),dwaterenta(0)
++ do i=1,398
++ read(iwaterwater,*) ract,awaterenta(i),bwaterenta(i),&
++ cwaterenta(i),dwaterenta(i)
++ irdiff=int((ract-2.06d0)*50.0d0)+1
++ if (i.ne.irdiff) print *,"WARTINING",i,ract, irdiff
++ enddo
++! water parmaters entrophy
++ read(iwaterwater,*) mychar
++ read(iwaterwater,*) ract,awaterentro(0),bwaterentro(0),&
++ cwaterentro(0),dwaterentro(0)
++ do i=1,398
++ read(iwaterwater,*) ract,awaterentro(i),bwaterentro(i),&
++ cwaterentro(i),dwaterentro(i)
++ irdiff=int((ract-2.06d0)*50.0d0)+1
++ if (i.ne.irdiff) print *,"WARTINING",i,ract, irdiff
++ enddo
++
#ifdef CRYST_THETA
!
allocate(ddnewtor(3,2,-nloctyp:nloctyp))
allocate(e0newtor(3,-nloctyp:nloctyp))
allocate(eenewtor(2,2,2,-nloctyp:nloctyp))
--
++ bnew1=0.0d0
++ bnew2=0.0d0
++ ccnew=0.0d0
++ ddnew=0.0d0
++ e0new=0.0d0
++ eenew=0.0d0
++ bnew1tor=0.0d0
++ bnew2tor=0.0d0
++ ccnewtor=0.0d0
++ ddnewtor=0.0d0
++ e0newtor=0.0d0
++ eenewtor=0.0d0
read (ifourier,*,end=115,err=115) (itype2loc(i),i=1,ntyp)
read (ifourier,*,end=115,err=115) (iloctyp(i),i=0,nloctyp-1)
itype2loc(ntyp1)=nloctyp
if (.not.allocated(chi2cat)) allocate(chi2cat(ntyp1,ntyp1)) !(ntyp,ntyp)
-- if (.not.allocated(ichargecat)) allocate (ichargecat(ntyp_molec(5)))
++ if (.not.allocated(ichargecat))&
++ allocate (ichargecat(-ntyp_molec(5):ntyp_molec(5)))
+ write(*,*) "before ions",oldion
++ ichargecat(:)=0
+
! i to SC, j to jon, isideocat - nazwa pliku z ktorego czytam parametry
if (oldion.eq.0) then
if (.not.allocated(icharge)) then ! this mean you are oprating in old sc-sc mode
else
read(iion,*) ijunk
endif
-
- do i=1,ntyp_molec(5)
+ print *,ntyp_molec(5)
- do i=1,ntyp_molec(5)
++ do i=-ntyp_molec(5),ntyp_molec(5)
read(iion,*) msc(i,5),restok(i,5),ichargecat(i)
print *,msc(i,5),restok(i,5)
enddo
endif ! unres_pdb
endif !firstion
read (card(12:16),*) atom
--! print *,"HETATOM", atom
++ print *,"HETATOM", atom(1:2)
read (card(18:20),'(a3)') res
++ if (atom(3:3).eq.'H') cycle
if ((atom(1:2).eq.'NA').or.(atom(1:2).eq.'CL').or.&
(atom(1:2).eq.'CA').or.(atom(1:2).eq.'MG') &
- .or.(atom(1:2).eq.'K '.or.(atom(1:2).eq.'ZN'))) &
- then
- .or.(atom(1:2).eq.'K ')) &
- then
++ .or.(atom(1:2).eq.'K ').or.(atom(1:2).eq.'ZN').or.&
++ (atom(1:2).eq.'O ')) then
ires=ires+1
++ print *,"I have water"
if (molecule.ne.5) molecprev=molecule
molecule=5
nres_molec(molecule)=nres_molec(molecule)+1
print *,"HERE",nres_molec(molecule)
-- res=res(2:3)//' '
++ if (res.ne.'WAT') res=res(2:3)//' '
itype(ires,molecule)=rescode(ires,res,0,molecule)
read(card(31:54),'(3f8.3)') (c(j,ires),j=1,3)
endif! NA
molnum(1)=5
itype(1,5)=itype(2,5)
itype(1,1)=0
-- do i=2,nres
++ do j=1,3
++ c(j,1)=c(j,2)
++ enddo
++ do i=2,nres-1
itype(i,5)=itype(i+1,5)
++ do j=1,3
++ c(j,i)=c(j,i+1)
++ enddo
enddo
itype(nres,5)=0
nres=nres-1
with_theta_constr = index(controlcard,"WITH_THETA_CONSTR").gt.0
protein=index(controlcard,"PROTEIN").gt.0
ions=index(controlcard,"IONS").gt.0
++ fodson=index(controlcard,"FODSON").gt.0
call readi(controlcard,'OLDION',oldion,1)
nucleic=index(controlcard,"NUCLEIC").gt.0
write (iout,*) "with_theta_constr ",with_theta_constr
call reada(controlcard,"YTUBE",tubecenter(2),0.0d0)
call reada(controlcard,"ZTUBE",tubecenter(3),0.0d0)
call reada(controlcard,"RTUBE",tubeR0,0.0d0)
++ call reada(controlcard,"VNANO",velnanoconst,0.0d0)
call reada(controlcard,"TUBETOP",bordtubetop,boxzsize)
call reada(controlcard,"TUBEBOT",bordtubebot,0.0d0)
call reada(controlcard,"TUBEBUF",tubebufthick,1.0d0)
call readi(controlcard,"NSTEP",n_timestep,1000000)
call readi(controlcard,"NTWE",ntwe,100)
call readi(controlcard,"NTWX",ntwx,1000)
++ call readi(controlcard,"NFOD",nfodstep,100)
call reada(controlcard,"DT",d_time,1.0d-1)
call reada(controlcard,"DVMAX",dvmax,2.0d1)
call reada(controlcard,"DAMAX",damax,1.0d1)
open (iion,file=ionname,status='old')
call getenv_loc('IONPAR_NUCL',ionnuclname)
open (iionnucl,file=ionnuclname,status='old')
+ call getenv_loc('IONPAR_TRAN',iontranname)
+ open (iiontran,file=iontranname,status='old')
++ call getenv_loc('WATWAT',iwaterwatername)
++ open (iwaterwater,file=iwaterwatername,status='old')
++ call getenv_loc('WATPROT',iwaterscname)
++ open (iwatersc,file=iwaterscname,status='old')
++
#else
open(1,file=pref_orig(:ilen(pref_orig))//'.inp',status='old',&
readonly)
open (iion,file=ionname,status='old',action='read')
call getenv_loc('IONPAR_NUCL',ionnuclname)
open (iionnucl,file=ionnuclname,status='old',action='read')
+ call getenv_loc('IONPAR_TRAN',iontranname)
+ open (iiontran,file=iontranname,status='old',action='read')
-
++ call getenv_loc('WATWAT',iwaterwatername)
++ open (iwaterwater,file=iwaterwatername,status='old',action='read')
++ call getenv_loc('WATPROT',iwaterscname)
++ open (iwatersc,file=iwaterscname,status='old',action='read')
#ifndef CRYST_SC
call getenv_loc('ROTPARPDB',rotname_pdb)
character(len=3) :: liczba
!el real(kind=8) :: qwolynes
!el external qwolynes
-- integer :: errmsg_count,maxerrmsg_count=100
++ integer :: errmsg_count,maxerrmsg_count=100000
!el real(kind=8) :: rmsnat,gyrate
!el external rmsnat,gyrate
-- real(kind=8) :: tole=1.0d-1
++ real(kind=8) :: tole=0.0d0
integer i,itj,ii,iii,j,k,l,licz
integer ir,ib,ipar,iparm
integer iscor,islice
ecation_prot, ecationcation,evdwpp,eespp,evdwpsb,eelpsb,evdwsb, &
eelsb,estr_nucl,ebe_nucl,esbloc,etors_nucl,etors_d_nucl,&
ecorr_nucl,ecorr3_nucl,escbase, epepbase,escpho, epeppho,ecation_nucl,&
- ehomology_constr
+ elipbond,elipang,eliplj,elipelec,ecat_prottran,ecation_protang, &
- eliptran
-
++ eliptran,ehomology_constr
integer :: i,ii,ik,iproc,iscor,j,k,l,ib,iparm,iprot,nlist
real(kind=8) :: qfree,sumprob,eini,efree,rmsdev
epepbase= enetb(47,i,iparm)
escbase= enetb(46,i,iparm)
ecation_nucl=enetb(50,i,iparm)
+ elipbond=enetb(52,i,iparm)
+ elipang=enetb(53,i,iparm)
+ eliplj=enetb(54,i,iparm)
+ elipelec=enetb(55,i,iparm)
+ ecat_prottran=enetb(56,i,iparm)
+ ecation_protang=enetb(57,i,iparm)
+ eliptran=enetb(22,i,iparm)
+ ehomology_constr=enetb(51,i,iparm)
+ if (homol_nset.gt.1) &
+ ehomology_constr=waga_homology(homol_nset)*ehomology_constr
! wscbase=ww(46)
! wpepbase=ww(47)
! wscpho=ww(48)
+wvdwpp_nucl*evdwpp+welpp*eespp+wvdwpsb*evdwpsb+welpsb*eelpsb&
+wvdwsb*evdwsb+welsb*eelsb+wsbloc*esbloc+wtor_nucl*etors_nucl&
+wtor_d_nucl*etors_d_nucl+wcorr_nucl*ecorr_nucl+wcorr3_nucl*ecorr3_nucl&
- +wscbase*escbase&
+ +wscbase*escbase+ehomology_constr&
+wpepbase*epepbase+wscpho*escpho+wpeppho*epeppho&
- +wcatnucl*ecation_nucl
+ +wcatnucl*ecation_nucl&
+ +elipbond+elipang+eliplj+elipelec+wcat_tran*ecat_prottran+ecation_protang+&
+ wliptran*eliptran
+
#else
etot=wsc*evdw+wscp*evdw2 &
+wvdwpp_nucl*evdwpp+welpp*eespp+wvdwpsb*evdwpsb+welpsb*eelpsb&
+wvdwsb*evdwsb+welsb*eelsb+wsbloc*esbloc+wtor_nucl*etors_nucl&
+wtor_d_nucl*etors_d_nucl+wcorr_nucl*ecorr_nucl+wcorr3_nucl*ecorr3_nucl&
- +wscbase*escbase&
+ +wscbase*escbase+ehomology_constr&
+wpepbase*epepbase+wscpho*escpho+wpeppho*epeppho&
- +wcatnucl*ecation_nucl
+ +wcatnucl*ecation_nucl&
+ +elipbond+elipang+eliplj+elipelec+wcat_tran*ecat_prottran+ecation_protang&
+ +wliptran*eliptran
+
+
#endif
enddo
enddo
endif
-- if (.not. allocated(msc)) allocate(msc(ntyp1,5))
-- if (.not. allocated(restok)) allocate(restok(ntyp1,5))
++ if (.not. allocated(msc)) allocate(msc(-ntyp1:ntyp1,5))
++ if (.not. allocated(restok)) allocate(restok(-ntyp1:ntyp1,5))
if (oldion.eq.1) then
do i=1,ntyp_molec(5)
if (.not.allocated(chi2cat)) allocate(chi2cat(ntyp1,ntyp1)) !(ntyp,ntyp)
-- allocate (ichargecat(ntyp_molec(5)))
++ allocate (ichargecat(-ntyp_molec(5):ntyp_molec(5)))
! i to SC, j to jon, isideocat - nazwa pliku z ktorego czytam parametry
if (oldion.eq.0) then
if (.not.allocated(icharge)) then ! this mean you are oprating in old sc-sc mode
read(iion,*) ijunk
endif
-- do i=1,ntyp_molec(5)
++ do i=-ntyp_molec(5),ntyp_molec(5)
read(iion,*) msc(i,5),restok(i,5),ichargecat(i)
print *,msc(i,5),restok(i,5)
enddo
subroutine read_general_data(*)
use control_data, only:indpdb,symetr,r_cut_ele,rlamb_ele,ions,&
- scelemode,TUBEmode,tor_mode,energy_dec
+ scelemode,TUBEmode,tor_mode,energy_dec,r_cut_ang,r_cut_mart,&
+ rlamb_mart
- use energy_data, only:distchainmax,tubeR0,tubecenter,dyn_ss
+ use energy_data, only:distchainmax,tubeR0,tubecenter,dyn_ss,constr_homology
use geometry_data, only:boxxsize,boxysize,boxzsize,bordtubetop,&
- bordtubebot,tubebufthick,buftubebot,buftubetop
+ bordtubebot,tubebufthick,buftubebot,buftubetop,buflipbot, bufliptop,bordlipbot,bordliptop, &
+ lipbufthick,lipthick
! implicit none
! include "DIMENSIONS"
! include "DIMENSIONS.ZSCOPT"
ecationcation,ecation_prot, evdwpp,eespp ,evdwpsb,eelpsb, &
evdwsb, eelsb, estr_nucl,ebe_nucl,esbloc,etors_nucl,etors_d_nucl,&
ecorr_nucl, ecorr3_nucl,epeppho, escpho, epepbase,escbase,ecation_nucl,&
- elipbond,elipang,eliplj,elipelec,ecat_prottran,ecation_protang,eliptran
-
- ehomology_constr,eliptran
++ elipbond,elipang,eliplj,elipelec,ecat_prottran,ecation_protang,eliptran,&
++ ehomology_constr
integer :: ind_point(maxpoint),upindE,indE
epepbase= enetb(47,i,iparm)
escbase= enetb(46,i,iparm)
ecation_nucl= enetb(50,i,iparm)
+ elipbond=enetb(52,i,iparm)
+ elipang=enetb(53,i,iparm)
+ eliplj=enetb(54,i,iparm)
+ elipelec=enetb(55,i,iparm)
+ ecat_prottran=enetb(56,i,iparm)
+ ecation_protang=enetb(57,i,iparm)
+ eliptran=enetb(22,i,iparm)
+ ehomology_constr=enetb(51,i,iparm)
#ifdef DEBUG
write (iout,'(3i5,6f5.2,15f12.3)') i,ib,iparm,(ft(l),l=1,6),&
evdw+evdw_t,evdw2,ees,evdw1,ecorr,eel_loc,estr,ebe,escloc,&
epepbase= enetb(47,i,iparm)
escbase= enetb(46,i,iparm)
ecation_nucl=enetb(50,i,iparm)
+ elipbond=enetb(52,i,iparm)
+ elipang=enetb(53,i,iparm)
+ eliplj=enetb(54,i,iparm)
+ elipelec=enetb(55,i,iparm)
+ ecat_prottran=enetb(56,i,iparm)
+ ecation_protang=enetb(57,i,iparm)
+ eliptran=enetb(22,i,iparm)
+ ehomology_constr=enetb(51,i,iparm)
#ifdef SPLITELE
etot=wsc*(evdw+ft(6)*evdw_t)+wscp*evdw2+ft(1)*welec*ees &
+wvdwpp*evdw1 &
epepbase= enetb(47,t,iparm)
escbase= enetb(46,t,iparm)
ecation_nucl=enetb(50,t,iparm)
+ elipbond=enetb(52,t,iparm)
+ elipang=enetb(53,t,iparm)
+ eliplj=enetb(54,t,iparm)
+ elipelec=enetb(55,t,iparm)
+ ecat_prottran=enetb(56,t,iparm)
+ ecation_protang=enetb(57,t,iparm)
+ eliptran=enetb(22,t,iparm)
+ ehomology_constr=enetb(51,t,iparm)
+
do k=0,nGridT
betaT=startGridT+k*delta_T
temper=betaT
projects / unres4.git / commitdiff