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wham is prining energies; all "good" changes seems to be revoked improve in rmsd...
authorAdam Sieradzan <adasko@piasek4.chem.univ.gda.pl>
Wed, 30 Mar 2016 08:16:35 +0000 (10:16 +0200)
committerAdam Sieradzan <adasko@piasek4.chem.univ.gda.pl>
Wed, 30 Mar 2016 08:16:35 +0000 (10:16 +0200)
PARAM/fourier_opt_iter0_7prot-eps.parm [new file with mode: 0644] patch | blob
PARAM/sc_GB_opt_iter0_7prot-eps.parm [new file with mode: 0644] patch | blob
PARAM/sc_GB_opt_iter0_7prot-eps_ext_lip.parm [new file with mode: 0644] patch | blob
PARAM/tor_opt_iter0_7prot-eps.parm [new file with mode: 0644] patch | blob
PARAM/torsion_631Gdp_old_ext.parm [new file with mode: 0644] patch | blob
PARAM/torsion_double_631Gdp_old_ext.parm [new file with mode: 0644] patch | blob
source/cluster/wham/src-M/energy_p_new.F patch | blob | history
source/unres/src_MD-M/energy_p_new_barrier.F patch | blob | history
source/wham/src-M/energy_p_new.F patch | blob | history
source/wham/src-M/read_ref_str.F patch | blob | history
source/wham/src-M/rmscalc.f patch | blob | history

diff --git a/PARAM/fourier_opt_iter0_7prot-eps.parm b/PARAM/fourier_opt_iter0_7prot-eps.parm
new file mode 100644 (file)
index 0000000..469881e
--- /dev/null
+++ b/PARAM/fourier_opt_iter0_7prot-eps.parm
@@ -0,0 +1,43 @@
+    3     # Number of local interaction types
+GLY
+   0.000000000000000
+   0.292273916587998
+   0.216221204139835
+   0.000000000000000
+   0.000000000000000
+   2.373462483972307
+  -0.927962753087420
+   0.000000000000000
+   0.000000000000000
+   1.365321421895682
+  -0.409536564749270
+   0.000000000000000
+   0.000000000000000
+CYS
+   0.000000000000000
+   0.250084847353610
+  -0.186158505094081
+  -0.504688747570979
+   1.218679171649523
+  -2.089734050079038
+   2.302365702770721
+  -0.532502145482045
+  -1.596421505165690
+   1.270543992159271
+   0.174687212656861
+  -0.599374829819892
+   0.222101519622321
+PRO
+   0.000000000000000
+  -0.787986560945931
+  -0.345208426278326
+  -1.111524460354935
+   0.530324242079397
+  -1.548870000000000
+   1.914370000000000
+   0.664143000000000
+  -0.454839000000000
+   0.448705912966141
+   0.346799067155216
+   0.311804899416344
+   0.230482726984751
diff --git a/PARAM/sc_GB_opt_iter0_7prot-eps.parm b/PARAM/sc_GB_opt_iter0_7prot-eps.parm
new file mode 100644 (file)
index 0000000..c18e501
--- /dev/null
+++ b/PARAM/sc_GB_opt_iter0_7prot-eps.parm
@@ -0,0 +1,74 @@
+    4    6
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+   3.729277869700000   2.294443648100000  -0.030356525500000   3.111577617700000
+  -0.082736296100000  -1.604311318200000   2.443983743500000  -4.389778328000000
+   2.366463453300000   4.192796926000000   2.674806001700000   2.699903447923231
+   2.969074945285474   2.893433539204819   3.025971784817564   2.862805741160594
+   2.526510086781303   2.424691603147259   2.468072853823478   2.397655578798363
+   2.574880627216491   2.408998508198888   2.430511884949466   2.449395893015385
+   2.498838549850558   2.499580191788341   2.377546242648636   2.327813161765345
+   2.406133938779852   2.703108539059061   4.927215476100000   5.503494126351864
+   4.145762376887038   4.785079589360221   2.768566455400537   3.578453064630948
+   7.377991203785909   7.384219593278416   2.013243866897712   0.798776956900000
+   4.098856348297708   2.235314730843289   3.228477565634609   3.304167710826445
+   2.495139323467606   2.159452467827879   6.270032209209654   7.373726105069984
+  14.031183976721900   2.686068179510170   0.869902301100000   1.480465743477956
+   1.049374502674771   1.027230702276932   1.034177551331201   0.913125966277553
+   0.945203407060163   0.729150916604920   1.061496950110300   1.242751812800000
+   0.840998362264854   1.917210204185132   1.040589435688749   1.612101630422405
+   1.325600429648876   1.718332060074302   0.762112976988035   0.905870718258032
+  26.496800489093268   0.876078821104577   0.010369755600000   0.061138567400000
+   0.044830334600000   0.039283178200000   0.085416633800000   0.039889661900000
+   0.024949656900000   0.023241090800000   0.086137910000000  -0.075479418500000
+  -0.026614602100000  -0.016342909900000   0.057216710300000  -0.046860882500000
+   0.015104845500000   0.008496367800000   0.027893039700000   0.007692291100000
+   0.103353673800000  -0.009825603600000
diff --git a/PARAM/sc_GB_opt_iter0_7prot-eps_ext_lip.parm b/PARAM/sc_GB_opt_iter0_7prot-eps_ext_lip.parm
new file mode 100644 (file)
index 0000000..a4e97f6
--- /dev/null
+++ b/PARAM/sc_GB_opt_iter0_7prot-eps_ext_lip.parm
@@ -0,0 +1,248 @@
+4  6
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+        6.2200032154        6.2159898496        5.2638423822        5.2638423822
+
+        6.6296746680        6.6717260508        6.8168876945        6.8378960152
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+   1.061496950110300   1.242751812800000   0.840998362264854   1.917210204185132
+   1.040589435688749   1.612101630422405   1.325600429648876   1.718332060074302
+   0.762112976988035   0.905870718258032  26.496800489093268   0.876078821104577
+        1.0540660014         .9385909298        1.0039962875        1.0039962875
+
+
+   0.010369755600000   0.061138567400000   0.044830334600000   0.039283178200000
+   0.085416633800000   0.039889661900000   0.024949656900000   0.023241090800000
+   0.086137910000000  -0.075479418500000  -0.026614602100000  -0.016342909900000
+   0.057216710300000  -0.046860882500000   0.015104845500000   0.008496367800000
+   0.027893039700000   0.007692291100000   0.103353673800000  -0.009825603600000
+         .0611385674         .0448303346         .0861379100         .0861379100
+
+
+   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    
+  
+   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    
+  
+   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    
+  
+   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    
+  
+   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    
+  
+   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    
+  
+   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    
+  
+   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    
+  
+   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    
+  
+  0.6888000       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    
+  
+   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    
+  
+   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    
+  
+   3.742000       3.448923       3.759161       3.467535    
+   3.782778       4.331384       3.744599       2.903442    
+   3.638776       4.527216       2.606238       2.606238    
+  
+   3.178800       3.464740       3.195954       3.486507    
+   3.992146       3.451319       2.676042       3.353784    
+   4.172640       2.402115       2.402115    
+
+   -7.2938        -4.0239         3.800125       5.9101
+   3.8743         2.916757       3.655463       4.547977
+   2.618191       2.618191
+
+  -3.0057         3.505321       6.0636         3.5303
+   2.690483       3.371882       4.195157       2.415078
+   2.415078
+
+   3.824000       4.378585       3.785405       2.935082
+   3.678429       4.576550       2.634640       2.634640
+
+  -0.1779        -3.4493         3.360749       4.211903
+   5.240276       3.016734       3.016734
+
+  -6.5557         2.905459       3.641304       4.530360
+   2.608049       2.608049
+
+   2.252800       2.823350       3.512697       2.022197
+   2.022197
+
+   3.538400       4.402332       2.534345       2.534345
+
+   5.477200       3.153127       3.153127
+
+   1.815200       1.815200
+
+   1.815200
+ 
diff --git a/PARAM/tor_opt_iter0_7prot-eps.parm b/PARAM/tor_opt_iter0_7prot-eps.parm
new file mode 100644 (file)
index 0000000..cd0a229
--- /dev/null
+++ b/PARAM/tor_opt_iter0_7prot-eps.parm
@@ -0,0 +1,252 @@
+3  ***  Optimized torsional parameters 7p_wham_last  ***  
+1 1 1 1 1 1 1 1 1 0 1 1 1 1 1 1 1 1 1 2 1 1 0 1
+6 0 ** Gly-D-Pro-reg
+     1                   -1.02141E+00      -1.21787E+00
+     2                    2.66194E-03       1.01052E-02
+     3                    1.41880E-02      -1.29145E-02
+     4                   -5.54912E-02      -1.54449E-02
+     5                    2.72669E-02       4.68748E-02
+     6                    7.92569E-03      -3.12502E-02
+6 0 ** Gly-D-Ala-reg
+     1                    9.97046E-02       2.66476E-01
+     2                   -1.69687E-02      -4.91316E-02
+     3                    2.50219E-01      -6.24989E-02
+     4                   -1.52445E-01      -1.24202E-01
+     5                   -9.21242E-03      -9.52846E-04
+     6                    6.34622E-03      -4.58307E-03
+ 6 0  ************  G-G
+     1                    2.91221E-01       0.00000E+00
+     2                    1.97221E-01       0.00000E+00
+     3                    3.47215E-02       0.00000E+00
+     4                   -1.25868E-01       0.00000E+00
+     5                   -8.07275E-02       0.00000E+00
+     6                   -3.07820E-03       0.00000E+00
+ 6 0  ************  G-A
+     1                    1.37258E-01      -1.87823E-01
+     2                   -3.24314E-03      -1.14115E-01
+     3                    1.00886E-01       6.20938E-02
+     4                   -1.24448E-01       1.61747E-01
+     5                   -1.22389E-02       1.29629E-01
+     6                    1.18244E-02      -7.32819E-02
+10 0  ************  G-P
+     1                   -2.35280E-01       4.47825E-01
+     2                    2.25332E-01       4.39143E-01
+     3                    8.54137E-02      -3.13391E-02
+     4                    9.34821E-04      -5.34886E-03
+     5                    1.29469E-01       2.38018E-01
+     6                   -1.67401E-01       1.36767E-01
+     7                   -9.09952E-03      -1.50380E-01
+     8                    1.59178E-01       1.58505E-02
+     9                   -5.07021E-02       9.02235E-02
+    10                   -2.74002E-02       3.70860E-02
+6 0 ** L-Ala-D-Pro-reg
+     1                   -3.67336E+00       1.98471E+00
+     2                   -6.26727E-01      -8.14864E-02
+     3                    2.43704E-02      -1.02431E+00
+     4                    3.16312E-01       1.87132E-01
+     5                    2.66420E-01       1.43927E-01
+     6                   -2.65977E-01       5.94169E-02
+6 0 ** L-Ala-D-Ala-reg
+     1                   -7.75462E-01       4.16758E-01
+     2                    2.23510E-02       6.78839E-02
+     3                    2.54868E-01      -8.31567E-02
+     4                   -7.10523E-02      -1.74577E-01
+     5                    3.33282E-02       3.98392E-02
+     6                    1.56054E-04      -1.41661E-02
+ 6 0  ************  A-G
+     1                   -2.29844E-01       8.10157E-02
+     2                   -7.16965E-02       8.72173E-02
+     3                    3.14208E-01      -5.35383E-02
+     4                   -2.02452E-01      -6.71549E-02
+     5                    6.37359E-02      -3.21902E-02
+     6                    1.20409E-02      -4.77091E-02
+ 6 0  ************  A-A
+     1                    4.84934E-01       1.01827E-01
+     2                    2.02908E-01      -1.57752E-01
+     3                    1.83892E-01      -9.11332E-03
+     4                   -5.50573E-02       3.62865E-02
+     5                    2.01397E-02       1.58844E-02
+     6                    6.37922E-03       2.45381E-03
+10 0  ************  A-P
+     1                    1.05440E+00       1.99420E+00
+     2                    4.15367E-01       2.58231E-01
+     3                    4.38811E-01       1.78360E-01
+     4                   -6.03233E-02       1.44596E-01
+     5                   -1.32748E-01      -8.30658E-02
+     6                    7.92515E-02      -1.23210E-01
+     7                    1.46959E-01       9.69035E-02
+     8                   -8.27696E-02       2.19985E-01
+     9                   -2.20971E-01       9.42558E-04
+    10                   -2.11828E-02      -3.91532E-02
+6 0 ** L-Pro-D-Pro-reg
+     1                   -3.40143E+00      -3.68917E+00
+     2                   -1.79356E+00       1.27378E+00
+     3                    1.52538E+00       1.51128E-01
+     4                   -1.16399E-01      -9.80625E-01
+     5                   -5.43709E-01       4.32254E-01
+     6                    3.39955E-01       1.28204E-01
+6 0 ** L-Pro-D-Ala-reg
+     1                   -7.91570E-01       1.00745E+00
+     2                    2.89816E-03      -1.42421E-01
+     3                    2.00092E-01      -1.46860E-01
+     4                    4.75906E-02       1.23842E-01
+     5                   -2.88990E-02      -2.23460E-02
+     6                    8.92327E-03      -2.80002E-02
+10 0  ************  P-G
+     1                    2.12359E-02       4.05506E-02
+     2                   -1.19424E-01       2.91087E-01
+     3                    3.81770E-01      -1.11839E-01
+     4                   -9.75339E-02      -7.60089E-02
+     5                   -5.00214E-02       3.42037E-02
+     6                    8.12296E-02       3.98713E-02
+     7                   -1.21613E-02      -4.57682E-02
+     8                    6.95870E-03       2.28245E-02
+     9                    2.02598E-02      -2.00100E-02
+    10                   -1.48685E-02      -1.09627E-02
+10 0  ************  P-A
+     1                   -5.30371E-01      -3.79838E-03
+     2                    6.32663E-02      -1.09521E-01
+     3                    1.21519E-01       8.43223E-03
+     4                   -7.80575E-03       3.76829E-02
+     5                   -4.82717E-02      -4.37033E-02
+     6                   -1.47599E-02       9.06497E-02
+     7                    4.59200E-02       2.27528E-02
+     8                   -7.44594E-02       4.24939E-02
+     9                   -4.90352E-02      -2.08349E-02
+    10                   -8.46346E-02      -1.07298E-02
+10 0  ************  P-P
+     1                    4.23486E+00       7.87119E-01
+     2                    2.59217E+00      -3.33044E-01
+     3                    1.24864E+00      -4.98088E-01
+     4                    1.16294E-01      -1.79001E-01
+     5                   -9.55402E-01       1.83034E-01
+     6                   -1.87536E+00       2.47282E-01
+     7                   -2.44663E+00       5.47506E-01
+     8                   -2.27142E+00       8.14203E-01
+     9                   -1.33942E+00       7.88906E-01
+    10                   -4.40969E-01       2.69137E-01
+6 0 ** Gly-D-Pro-reg
+     1                   -1.02141E+00      -1.21787E+00
+     2                    2.66194E-03       1.01052E-02
+     3                    1.41880E-02      -1.29145E-02
+     4                   -5.54912E-02      -1.54449E-02
+     5                    2.72669E-02       4.68748E-02
+     6                    7.92569E-03      -3.12502E-02
+6 0 ** Gly-D-Ala-reg
+     1                    9.97046E-02       2.66476E-01
+     2                   -1.69687E-02      -4.91316E-02
+     3                    2.50219E-01      -6.24989E-02
+     4                   -1.52445E-01      -1.24202E-01
+     5                   -9.21242E-03      -9.52846E-04
+     6                    6.34622E-03      -4.58307E-03
+ 6 0  ************  G-G
+     1                    2.91221E-01       0.00000E+00
+     2                    1.97221E-01       0.00000E+00
+     3                    3.47215E-02       0.00000E+00
+     4                   -1.25868E-01       0.00000E+00
+     5                   -8.07275E-02       0.00000E+00
+     6                   -3.07820E-03       0.00000E+00
+ 6 0  ************  G-A
+     1                    1.37258E-01      -1.87823E-01
+     2                   -3.24314E-03      -1.14115E-01
+     3                    1.00886E-01       6.20938E-02
+     4                   -1.24448E-01       1.61747E-01
+     5                   -1.22389E-02       1.29629E-01
+     6                    1.18244E-02      -7.32819E-02
+10 0  ************  G-P
+     1                   -2.35280E-01       4.47825E-01
+     2                    2.25332E-01       4.39143E-01
+     3                    8.54137E-02      -3.13391E-02
+     4                    9.34821E-04      -5.34886E-03
+     5                    1.29469E-01       2.38018E-01
+     6                   -1.67401E-01       1.36767E-01
+     7                   -9.09952E-03      -1.50380E-01
+     8                    1.59178E-01       1.58505E-02
+     9                   -5.07021E-02       9.02235E-02
+    10                   -2.74002E-02       3.70860E-02
+6 0 ** L-Ala-D-Pro-reg
+     1                   -3.67336E+00       1.98471E+00
+     2                   -6.26727E-01      -8.14864E-02
+     3                    2.43704E-02      -1.02431E+00
+     4                    3.16312E-01       1.87132E-01
+     5                    2.66420E-01       1.43927E-01
+     6                   -2.65977E-01       5.94169E-02
+6 0 ** L-Ala-D-Ala-reg
+     1                   -7.75462E-01       4.16758E-01
+     2                    2.23510E-02       6.78839E-02
+     3                    2.54868E-01      -8.31567E-02
+     4                   -7.10523E-02      -1.74577E-01
+     5                    3.33282E-02       3.98392E-02
+     6                    1.56054E-04      -1.41661E-02
+ 6 0  ************  A-G
+     1                   -2.29844E-01       8.10157E-02
+     2                   -7.16965E-02       8.72173E-02
+     3                    3.14208E-01      -5.35383E-02
+     4                   -2.02452E-01      -6.71549E-02
+     5                    6.37359E-02      -3.21902E-02
+     6                    1.20409E-02      -4.77091E-02
+ 6 0  ************  A-A
+     1                    4.84934E-01       1.01827E-01
+     2                    2.02908E-01      -1.57752E-01
+     3                    1.83892E-01      -9.11332E-03
+     4                   -5.50573E-02       3.62865E-02
+     5                    2.01397E-02       1.58844E-02
+     6                    6.37922E-03       2.45381E-03
+10 0  ************  A-P
+     1                    1.05440E+00       1.99420E+00
+     2                    4.15367E-01       2.58231E-01
+     3                    4.38811E-01       1.78360E-01
+     4                   -6.03233E-02       1.44596E-01
+     5                   -1.32748E-01      -8.30658E-02
+     6                    7.92515E-02      -1.23210E-01
+     7                    1.46959E-01       9.69035E-02
+     8                   -8.27696E-02       2.19985E-01
+     9                   -2.20971E-01       9.42558E-04
+    10                   -2.11828E-02      -3.91532E-02
+6 0 ** L-Pro-D-Pro-reg
+     1                   -3.40143E+00      -3.68917E+00
+     2                   -1.79356E+00       1.27378E+00
+     3                    1.52538E+00       1.51128E-01
+     4                   -1.16399E-01      -9.80625E-01
+     5                   -5.43709E-01       4.32254E-01
+     6                    3.39955E-01       1.28204E-01
+6 0 ** L-Pro-D-Ala-reg
+     1                   -7.91570E-01       1.00745E+00
+     2                    2.89816E-03      -1.42421E-01
+     3                    2.00092E-01      -1.46860E-01
+     4                    4.75906E-02       1.23842E-01
+     5                   -2.88990E-02      -2.23460E-02
+     6                    8.92327E-03      -2.80002E-02
+10 0  ************  P-G
+     1                    2.12359E-02       4.05506E-02
+     2                   -1.19424E-01       2.91087E-01
+     3                    3.81770E-01      -1.11839E-01
+     4                   -9.75339E-02      -7.60089E-02
+     5                   -5.00214E-02       3.42037E-02
+     6                    8.12296E-02       3.98713E-02
+     7                   -1.21613E-02      -4.57682E-02
+     8                    6.95870E-03       2.28245E-02
+     9                    2.02598E-02      -2.00100E-02
+    10                   -1.48685E-02      -1.09627E-02
+10 0  ************  P-A
+     1                   -5.30371E-01      -3.79838E-03
+     2                    6.32663E-02      -1.09521E-01
+     3                    1.21519E-01       8.43223E-03
+     4                   -7.80575E-03       3.76829E-02
+     5                   -4.82717E-02      -4.37033E-02
+     6                   -1.47599E-02       9.06497E-02
+     7                    4.59200E-02       2.27528E-02
+     8                   -7.44594E-02       4.24939E-02
+     9                   -4.90352E-02      -2.08349E-02
+    10                   -8.46346E-02      -1.07298E-02
+10 0  ************  P-P
+     1                    4.23486E+00       7.87119E-01
+     2                    2.59217E+00      -3.33044E-01
+     3                    1.24864E+00      -4.98088E-01
+     4                    1.16294E-01      -1.79001E-01
+     5                   -9.55402E-01       1.83034E-01
+     6                   -1.87536E+00       2.47282E-01
+     7                   -2.44663E+00       5.47506E-01
+     8                   -2.27142E+00       8.14203E-01
+     9                   -1.33942E+00       7.88906E-01
+    10                   -4.40969E-01       2.69137E-01
diff --git a/PARAM/torsion_631Gdp_old_ext.parm b/PARAM/torsion_631Gdp_old_ext.parm
new file mode 100644 (file)
index 0000000..09d5df7
--- /dev/null
+++ b/PARAM/torsion_631Gdp_old_ext.parm
@@ -0,0 +1,180 @@
+3  *** Parameters derived by integrating MP2/6-31G** local energy surfaces ***
+1 1 1 1 1 1 1 1 1 0 1 1 1 1 1 1 1 1 1 2 1 1 0 0
+ 0 0 ** Gly-D-Pro-reg
+ 0 0 ** Gly-D-Ala-reg
+ 6 0 ************ G-G
+     1                    4.03053E-03       0.0
+     2                   -4.90330E-03       0.0
+     3                    2.70952E-01       0.0
+     4                   -7.20927E-02       0.0
+     5                   -3.66258E-03       0.0
+     6                   -6.34294E-03       0.0
+ 6 0 ************ G-A
+     1                    1.27465E-02      -1.01763E-01
+     2                   -8.41985E-03       1.18716E-02
+     3                    2.50582E-01       3.30235E-02
+     4                   -1.02631E-01       1.46337E-01
+     5                    6.63161E-03       8.86275E-03
+     6                   -6.81049E-03       8.71641E-03
+10 0 ************ G-P
+     1                   -1.14953E+00       1.29720E+00
+     2                   -1.08859E-03      -1.20321E-02
+     3                    4.04229E-01       2.92750E-01
+     4                   -2.41994E-01       5.38295E-02
+     5                    4.31804E-02      -6.56306E-02
+     6                    4.29080E-02       1.38685E-01
+     7                   -6.31286E-02      -2.65338E-02
+     8                    1.46743E-02      -3.26658E-03
+     9                   -1.33460E-02       3.01470E-02
+     0                   -1.11258E-02      -3.15723E-02
+ 0 0 ****** Ala-D-Pro
+ 0 0 ****** Ala-D-Ala
+ 6 0 ************ A-G
+     1                    5.14830E-03       9.48478E-02
+     2                   -8.85552E-02       1.20661E-01
+     3                    2.65903E-01      -8.99192E-02
+     4                   -6.16552E-02      -6.07952E-02
+     5                    2.19209E-02      -3.09487E-02
+     6                   -1.58136E-02      -1.74252E-02
+ 6 0 ************ A-A
+     1                    1.05084E+00      -1.83406E-03
+     2                    2.56198E-01       3.75825E-02
+     3                    2.97224E-01      -6.65886E-03
+     4                   -9.30144E-02       2.78499E-02
+     5                    2.69127E-02      -2.79813E-03
+     6                   -5.69348E-03      -5.76679E-03
+10 0 ************ A-P
+     1                    1.97348E+00       3.61809E+00
+     2                    3.25172E-01       6.93324E-01
+     3                    7.44811E-01       2.28853E-01
+     4                   -1.11515E-02       4.21766E-01
+     5                   -1.09160E-01       4.09945E-02
+     6                    1.08618E-01       6.71048E-03
+     7                    1.21785E-02       9.37813E-02
+     8                   -2.77282E-02       2.84981E-02
+     9                    2.15879E-02       1.85528E-02
+     0                   -8.56980E-03       3.92482E-02
+ 0 0 ** Pro-D-Por
+ 0 0 ** Pro-D-Ala
+10 0 ************ P-G
+     1                    2.12359E-02       4.05506E-02
+     2                   -1.19424E-01       2.91087E-01
+     3                    3.81770E-01      -1.11839E-01
+     4                   -9.75339E-02      -7.60089E-02
+     5                   -5.00214E-02       3.42037E-02
+     6                    8.12296E-02       3.98713E-02
+     7                   -1.21613E-02      -4.57682E-02
+     8                    6.95870E-03       2.28245E-02
+     9                    2.02598E-02      -2.00100E-02
+     0                   -1.48685E-02      -1.09627E-02
+10 0 ************ P-A
+     1                    1.40539E+00      -7.42879E-01
+     2                    9.21075E-02      -1.17205E-01
+     3                    4.49479E-01       3.82888E-02
+     4                    8.11975E-02      -3.35594E-02
+     5                   -9.88964E-03      -4.63759E-02
+     6                    8.58396E-02       4.22362E-02
+     7                    2.73049E-02      -5.43392E-02
+     8                   -4.18620E-03      -1.04889E-02
+     9                    1.06804E-02      -7.89066E-03
+     0                   -5.01879E-03      -1.20569E-02
+10 0 ************ P-P
+     1                    4.23219E+00       1.42318E+00
+     2                    1.24967E+00      -2.32575E-01
+     3                    5.38690E-01      -4.25507E-01
+     4                    4.01096E-01      -6.42186E-01
+     5                    2.52852E-01      -2.32257E-01
+     6                   -3.06406E-02      -2.48617E-01
+     7                   -1.68086E-02      -1.55069E-01
+     8                   -9.68421E-02      -1.80718E-01
+     9                   -2.73541E-02      -1.36915E-01
+     0                   -6.08829E-02      -6.71426E-02
+ 0 0 ** Gly-D-Pro-reg
+ 0 0 ** Gly-D-Ala-reg
+ 6 0 ************ G-G
+     1                    4.03053E-03       0.0
+     2                   -4.90330E-03       0.0
+     3                    2.70952E-01       0.0
+     4                   -7.20927E-02       0.0
+     5                   -3.66258E-03       0.0
+     6                   -6.34294E-03       0.0
+ 6 0 ************ G-A
+     1                    1.27465E-02      -1.01763E-01
+     2                   -8.41985E-03       1.18716E-02
+     3                    2.50582E-01       3.30235E-02
+     4                   -1.02631E-01       1.46337E-01
+     5                    6.63161E-03       8.86275E-03
+     6                   -6.81049E-03       8.71641E-03
+10 0 ************ G-P
+     1                   -1.14953E+00       1.29720E+00
+     2                   -1.08859E-03      -1.20321E-02
+     3                    4.04229E-01       2.92750E-01
+     4                   -2.41994E-01       5.38295E-02
+     5                    4.31804E-02      -6.56306E-02
+     6                    4.29080E-02       1.38685E-01
+     7                   -6.31286E-02      -2.65338E-02
+     8                    1.46743E-02      -3.26658E-03
+     9                   -1.33460E-02       3.01470E-02
+     0                   -1.11258E-02      -3.15723E-02
+ 0 0 ****** Ala-D-Pro
+ 0 0 ****** Ala-D-Ala
+ 6 0 ************ A-G
+     1                    5.14830E-03       9.48478E-02
+     2                   -8.85552E-02       1.20661E-01
+     3                    2.65903E-01      -8.99192E-02
+     4                   -6.16552E-02      -6.07952E-02
+     5                    2.19209E-02      -3.09487E-02
+     6                   -1.58136E-02      -1.74252E-02
+ 6 0 ************ A-A
+     1                    1.05084E+00      -1.83406E-03
+     2                    2.56198E-01       3.75825E-02
+     3                    2.97224E-01      -6.65886E-03
+     4                   -9.30144E-02       2.78499E-02
+     5                    2.69127E-02      -2.79813E-03
+     6                   -5.69348E-03      -5.76679E-03
+10 0 ************ A-P
+     1                    1.97348E+00       3.61809E+00
+     2                    3.25172E-01       6.93324E-01
+     3                    7.44811E-01       2.28853E-01
+     4                   -1.11515E-02       4.21766E-01
+     5                   -1.09160E-01       4.09945E-02
+     6                    1.08618E-01       6.71048E-03
+     7                    1.21785E-02       9.37813E-02
+     8                   -2.77282E-02       2.84981E-02
+     9                    2.15879E-02       1.85528E-02
+     0                   -8.56980E-03       3.92482E-02
+ 0 0 ** Pro-D-Por
+ 0 0 ** Pro-D-Ala
+10 0 ************ P-G
+     1                    2.12359E-02       4.05506E-02
+     2                   -1.19424E-01       2.91087E-01
+     3                    3.81770E-01      -1.11839E-01
+     4                   -9.75339E-02      -7.60089E-02
+     5                   -5.00214E-02       3.42037E-02
+     6                    8.12296E-02       3.98713E-02
+     7                   -1.21613E-02      -4.57682E-02
+     8                    6.95870E-03       2.28245E-02
+     9                    2.02598E-02      -2.00100E-02
+     0                   -1.48685E-02      -1.09627E-02
+10 0 ************ P-A
+     1                    1.40539E+00      -7.42879E-01
+     2                    9.21075E-02      -1.17205E-01
+     3                    4.49479E-01       3.82888E-02
+     4                    8.11975E-02      -3.35594E-02
+     5                   -9.88964E-03      -4.63759E-02
+     6                    8.58396E-02       4.22362E-02
+     7                    2.73049E-02      -5.43392E-02
+     8                   -4.18620E-03      -1.04889E-02
+     9                    1.06804E-02      -7.89066E-03
+     0                   -5.01879E-03      -1.20569E-02
+10 0 ************ P-P
+     1                    4.23219E+00       1.42318E+00
+     2                    1.24967E+00      -2.32575E-01
+     3                    5.38690E-01      -4.25507E-01
+     4                    4.01096E-01      -6.42186E-01
+     5                    2.52852E-01      -2.32257E-01
+     6                   -3.06406E-02      -2.48617E-01
+     7                   -1.68086E-02      -1.55069E-01
+     8                   -9.68421E-02      -1.80718E-01
+     9                   -2.73541E-02      -1.36915E-01
+     0                   -6.08829E-02      -6.71426E-02
diff --git a/PARAM/torsion_double_631Gdp_old_ext.parm b/PARAM/torsion_double_631Gdp_old_ext.parm
new file mode 100644 (file)
index 0000000..9eb0747
--- /dev/null
+++ b/PARAM/torsion_double_631Gdp_old_ext.parm
@@ -0,0 +1,5317 @@
+Gpp
+0 0
+ 0 0
+ 0 0
+ 0 0
+ 0 0 
+ 0 0
+Gpa
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+1.28857E-03
+5.46137E-03
+-2.15724E-01
+2.27414E-01
+9.50069E-02
+-1.60267E-01
+-1.77017E-01
+-1.06693E-01
+
diff --git a/source/cluster/wham/src-M/energy_p_new.F b/source/cluster/wham/src-M/energy_p_new.F
index 18a075c..a71e55b 100644 (file)
--- a/source/cluster/wham/src-M/energy_p_new.F
+++ b/source/cluster/wham/src-M/energy_p_new.F
@@ -112,6 +112,11 @@ c         print *,"calling multibody_eello"
          call multibody_eello(ecorr,ecorr5,ecorr6,eturn6,n_corr,n_corr1)
 c         write (*,*) 'n_corr=',n_corr,' n_corr1=',n_corr1
 c         print *,ecorr,ecorr5,ecorr6,eturn6
+      else
+         ecorr=0.0d0
+         ecorr5=0.0d0
+         ecorr6=0.0d0
+         eturn6=0.0d0
       endif
       if (wcorr4.eq.0.0d0 .and. wcorr.gt.0.0d0) then
          call multibody_hb(ecorr,ecorr5,ecorr6,n_corr,n_corr1)
@@ -2206,7 +2211,7 @@ C         endif
         num_conti=0
 c        write (iout,*) 'i',i,' ielstart',ielstart(i),' ielend',ielend(i)
         do j=ielstart(i),ielend(i)
-          if (j.le.1) cycle
+C          if (j.le.1) cycle
 C           if (itype(j).eq.ntyp1 .or. itype(j+1).eq.ntyp1
 C     & .or.itype(j+2).eq.ntyp1
 C     &) cycle
diff --git a/source/unres/src_MD-M/energy_p_new_barrier.F b/source/unres/src_MD-M/energy_p_new_barrier.F
index aafba26..4a47935 100644 (file)
--- a/source/unres/src_MD-M/energy_p_new_barrier.F
+++ b/source/unres/src_MD-M/energy_p_new_barrier.F
@@ -3593,7 +3593,7 @@ C I TU KURWA
         do j=ielstart(i),ielend(i)
 C          do j=16,17
 C          write (iout,*) i,j
-         if (j.le.1) cycle
+C         if (j.le.1) cycle
           if (itype(j).eq.ntyp1.or. itype(j+1).eq.ntyp1
 C changes suggested by Ana to avoid out of bounds
 c     & .or.((j+2).gt.nres)
@@ -3801,6 +3801,7 @@ cd     &      xmedi,ymedi,zmedi,xj,yj,zj
               write (iout,'(a6,2i5,0pf7.3,2i5,2e11.3)') 
      &'evdw1',i,j,evdwij
      &,iteli,itelj,aaa,evdw1
+              write (iout,*) sss
               write (iout,'(a6,2i5,0pf7.3,2f8.3)') 'ees',i,j,eesij,
      &fac_shield(i),fac_shield(j)
           endif
diff --git a/source/wham/src-M/energy_p_new.F b/source/wham/src-M/energy_p_new.F
index fb18913..a57f604 100644 (file)
--- a/source/wham/src-M/energy_p_new.F
+++ b/source/wham/src-M/energy_p_new.F
@@ -2174,7 +2174,7 @@ C         endif
         num_conti=0
 C        write (iout,*) 'i',i,' ielstart',ielstart(i),' ielend',ielend(i)
         do j=ielstart(i),ielend(i)
-          if (j.le.1) cycle
+          if (j.lt.1) cycle
 C           if (itype(j).eq.ntyp1 .or. itype(j+1).eq.ntyp1
 C     & .or.itype(j+2).eq.ntyp1
 C     &) cycle  
diff --git a/source/wham/src-M/read_ref_str.F b/source/wham/src-M/read_ref_str.F
index 292fa02..6473d95 100644 (file)
--- a/source/wham/src-M/read_ref_str.F
+++ b/source/wham/src-M/read_ref_str.F
@@ -167,6 +167,7 @@ c      print *,"Calling elecont"
      &    'Number of residues to be superposed:',nsup,
      &    ' (from residue',nstart_sup,' to residue',
      &    nend_sup,').'
+      nres=nres0
       nnt=nnt_old
       nct=nct_old
       return
diff --git a/source/wham/src-M/rmscalc.f b/source/wham/src-M/rmscalc.f
index eecf900..638fd81 100644 (file)
--- a/source/wham/src-M/rmscalc.f
+++ b/source/wham/src-M/rmscalc.f
@@ -155,12 +155,16 @@ c-------------------------------------------------------------------------
       rminrms=10.0d10
       rmsminsing=10d10
       nperm=1
+C      write (iout,*) "tu2", nres,nsup
+      noverlap=nres
+      if (nres.gt.nsup) noverlap=nsup
+      write (iout,*) "tu3,",noverlap
       do i=1,symetr
        nperm=nperm*i
       enddo
       do kkk=1,nperm
        nnsup=0
-       do i=1,nres
+       do i=1,noverlap
         if (itype(i).ne.ntyp1) then
           nnsup=nnsup+1
           do j=1,3
UNRESPACK 3.x