2 implicit real*8 (a-h,o-z)
8 include 'COMMON.CONTROL'
9 include 'COMMON.SBRIDGE'
10 include 'COMMON.IOUNITS'
12 C Read force-field parameters except weights
14 C Read job setup parameters
16 C Read control parameters for energy minimzation if required
17 if (minim) call read_minim
18 C Read MCM control parameters if required
19 if (modecalc.eq.3 .or. modecalc.eq.6) call mcmread
20 C Read MD control parameters if reqjuired
21 if (modecalc.eq.12) call read_MDpar
22 C Read MREMD control parameters if required
23 if (modecalc.eq.14) then
27 C Read MUCA control parameters if required
28 if (lmuca) call read_muca
29 C Read CSA control parameters if required (from fort.40 if exists
30 C otherwise from general input file)
31 if (modecalc.eq.8) then
32 inquire (file="fort.40",exist=file_exist)
33 if (.not.file_exist) call csaread
35 cfmc if (modecalc.eq.10) call mcmfread
36 C Read molecule information, molecule geometry, energy-term weights, and
37 C restraints if requested
39 C Print restraint information
41 if (.not. out1file .or. me.eq.king) then
44 &write (iout,'(a,i5,a)') "The following",nhpb-nss,
45 & " distance constraints have been imposed"
47 write (iout,'(3i6,f10.5)') i-nss,ihpb(i),jhpb(i),forcon(i)
52 c print *,"Processor",myrank," leaves READRTNS"
55 C-------------------------------------------------------------------------------
56 subroutine read_control
60 implicit real*8 (a-h,o-z)
64 logical OKRandom, prng_restart
67 include 'COMMON.IOUNITS'
68 include 'COMMON.TIME1'
69 include 'COMMON.THREAD'
70 include 'COMMON.SBRIDGE'
71 include 'COMMON.CONTROL'
74 include 'COMMON.HEADER'
76 include 'COMMON.CHAIN'
79 include 'COMMON.FFIELD'
80 include 'COMMON.INTERACT'
81 include 'COMMON.SETUP'
82 COMMON /MACHSW/ KDIAG,ICORFL,IXDR
83 character*8 diagmeth(0:3) /'Library','EVVRSP','Givens','Jacobi'/
85 character*320 controlcard
90 read (INP,'(a)') titel
91 call card_concat(controlcard)
92 c out1file=index(controlcard,'OUT1FILE').gt.0 .or. fg_rank.gt.0
93 c print *,"Processor",me," fg_rank",fg_rank," out1file",out1file
94 call reada(controlcard,'SEED',seed,0.0D0)
95 call random_init(seed)
96 C Set up the time limit (caution! The time must be input in minutes!)
97 read_cart=index(controlcard,'READ_CART').gt.0
98 call readi(controlcard,'CONSTR_DIST',constr_dist,0)
99 call readi(controlcard,'SYM',symetr,1)
100 call reada(controlcard,'TIMLIM',timlim,960.0D0) ! default 16 hours
101 unres_pdb = index(controlcard,'UNRES_PDB') .gt. 0
102 call reada(controlcard,'SAFETY',safety,30.0D0) ! default 30 minutes
103 call reada(controlcard,'RMSDBC',rmsdbc,3.0D0)
104 call reada(controlcard,'RMSDBC1',rmsdbc1,0.5D0)
105 call reada(controlcard,'RMSDBC1MAX',rmsdbc1max,1.5D0)
106 call reada(controlcard,'RMSDBCM',rmsdbcm,3.0D0)
107 call reada(controlcard,'DRMS',drms,0.1D0)
108 if(me.eq.king .or. .not. out1file .and. fg_rank.eq.0) then
109 write (iout,'(a,f10.1)')'RMSDBC = ',rmsdbc
110 write (iout,'(a,f10.1)')'RMSDBC1 = ',rmsdbc1
111 write (iout,'(a,f10.1)')'RMSDBC1MAX = ',rmsdbc1max
112 write (iout,'(a,f10.1)')'DRMS = ',drms
113 write (iout,'(a,f10.1)')'RMSDBCM = ',rmsdbcm
114 write (iout,'(a,f10.1)') 'Time limit (min):',timlim
116 call readi(controlcard,'NZ_START',nz_start,0)
117 call readi(controlcard,'NZ_END',nz_end,0)
118 call readi(controlcard,'IZ_SC',iz_sc,0)
120 safety = 60.0d0*safety
123 call reada(controlcard,"T_BATH",t_bath,300.0d0)
124 minim=(index(controlcard,'MINIMIZE').gt.0)
125 dccart=(index(controlcard,'CART').gt.0)
126 overlapsc=(index(controlcard,'OVERLAP').gt.0)
127 overlapsc=.not.overlapsc
128 searchsc=(index(controlcard,'NOSEARCHSC').gt.0)
129 searchsc=.not.searchsc
130 sideadd=(index(controlcard,'SIDEADD').gt.0)
131 energy_dec=(index(controlcard,'ENERGY_DEC').gt.0)
132 outpdb=(index(controlcard,'PDBOUT').gt.0)
133 outmol2=(index(controlcard,'MOL2OUT').gt.0)
134 pdbref=(index(controlcard,'PDBREF').gt.0)
135 refstr=pdbref .or. (index(controlcard,'REFSTR').gt.0)
136 indpdb=index(controlcard,'PDBSTART')
137 extconf=(index(controlcard,'EXTCONF').gt.0)
138 call readi(controlcard,'IPRINT',iprint,0)
139 call readi(controlcard,'MAXGEN',maxgen,10000)
140 call readi(controlcard,'MAXOVERLAP',maxoverlap,1000)
141 call readi(controlcard,"KDIAG",kdiag,0)
142 call readi(controlcard,"RESCALE_MODE",rescale_mode,2)
143 if(me.eq.king .or. .not. out1file .and. fg_rank.eq.0)
144 & write (iout,*) "RESCALE_MODE",rescale_mode
145 split_ene=index(controlcard,'SPLIT_ENE').gt.0
146 if (index(controlcard,'REGULAR').gt.0.0D0) then
147 call reada(controlcard,'WEIDIS',weidis,0.1D0)
151 if (index(controlcard,'CHECKGRAD').gt.0) then
153 if (index(controlcard,'CART').gt.0) then
155 elseif (index(controlcard,'CARINT').gt.0) then
160 elseif (index(controlcard,'THREAD').gt.0) then
162 call readi(controlcard,'THREAD',nthread,0)
163 if (nthread.gt.0) then
164 call reada(controlcard,'WEIDIS',weidis,0.1D0)
167 & write (iout,'(a)')'A number has to follow the THREAD keyword.'
168 stop 'Error termination in Read_Control.'
170 else if (index(controlcard,'MCMA').gt.0) then
172 else if (index(controlcard,'MCEE').gt.0) then
174 else if (index(controlcard,'MULTCONF').gt.0) then
176 else if (index(controlcard,'MAP').gt.0) then
178 call readi(controlcard,'MAP',nmap,0)
179 else if (index(controlcard,'CSA').gt.0) then
181 crc else if (index(controlcard,'ZSCORE').gt.0) then
183 crc ZSCORE is rm from UNRES, modecalc=9 is available
186 cfcm else if (index(controlcard,'MCMF').gt.0) then
188 else if (index(controlcard,'SOFTREG').gt.0) then
190 else if (index(controlcard,'CHECK_BOND').gt.0) then
192 else if (index(controlcard,'TEST').gt.0) then
194 else if (index(controlcard,'MD').gt.0) then
196 else if (index(controlcard,'RE ').gt.0) then
200 lmuca=index(controlcard,'MUCA').gt.0
201 call readi(controlcard,'MUCADYN',mucadyn,0)
202 call readi(controlcard,'MUCASMOOTH',muca_smooth,0)
203 if (lmuca .and. (me.eq.king .or. .not.out1file ))
205 write (iout,*) 'MUCADYN=',mucadyn
206 write (iout,*) 'MUCASMOOTH=',muca_smooth
209 iscode=index(controlcard,'ONE_LETTER')
210 indphi=index(controlcard,'PHI')
211 indback=index(controlcard,'BACK')
212 iranconf=index(controlcard,'RAND_CONF')
213 i2ndstr=index(controlcard,'USE_SEC_PRED')
214 gradout=index(controlcard,'GRADOUT').gt.0
215 gnorm_check=index(controlcard,'GNORM_CHECK').gt.0
216 call reada(controlcard,'DISTCHAINMAX',distchainmax,5.0d0)
217 if (me.eq.king .or. .not.out1file )
218 & write (iout,*) "DISTCHAINMAX",distchainmax
220 if(me.eq.king.or..not.out1file)
221 & write (iout,'(2a)') diagmeth(kdiag),
222 & ' routine used to diagonalize matrices.'
225 c--------------------------------------------------------------------------
226 subroutine read_REMDpar
230 implicit real*8 (a-h,o-z)
232 include 'COMMON.IOUNITS'
233 include 'COMMON.TIME1'
236 include 'COMMON.LANGEVIN'
238 include 'COMMON.LANGEVIN.lang0'
240 include 'COMMON.INTERACT'
241 include 'COMMON.NAMES'
243 include 'COMMON.REMD'
244 include 'COMMON.CONTROL'
245 include 'COMMON.SETUP'
247 character*320 controlcard
248 character*3200 controlcard1
249 integer iremd_m_total
251 if(me.eq.king.or..not.out1file)
252 & write (iout,*) "REMD setup"
254 call card_concat(controlcard)
255 call readi(controlcard,"NREP",nrep,3)
256 call readi(controlcard,"NSTEX",nstex,1000)
257 call reada(controlcard,"RETMIN",retmin,10.0d0)
258 call reada(controlcard,"RETMAX",retmax,1000.0d0)
259 mremdsync=(index(controlcard,'SYNC').gt.0)
260 call readi(controlcard,"NSYN",i_sync_step,100)
261 restart1file=(index(controlcard,'REST1FILE').gt.0)
262 traj1file=(index(controlcard,'TRAJ1FILE').gt.0)
263 call readi(controlcard,"TRAJCACHE",max_cache_traj_use,1)
264 if(max_cache_traj_use.gt.max_cache_traj)
265 & max_cache_traj_use=max_cache_traj
266 if(me.eq.king.or..not.out1file) then
267 cd if (traj1file) then
268 crc caching is in testing - NTWX is not ignored
269 cd write (iout,*) "NTWX value is ignored"
270 cd write (iout,*) " trajectory is stored to one file by master"
271 cd write (iout,*) " before exchange at NSTEX intervals"
273 write (iout,*) "NREP= ",nrep
274 write (iout,*) "NSTEX= ",nstex
275 write (iout,*) "SYNC= ",mremdsync
276 write (iout,*) "NSYN= ",i_sync_step
277 write (iout,*) "TRAJCACHE= ",max_cache_traj_use
280 if (index(controlcard,'TLIST').gt.0) then
282 call card_concat(controlcard1)
283 read(controlcard1,*) (remd_t(i),i=1,nrep)
284 if(me.eq.king.or..not.out1file)
285 & write (iout,*)'tlist',(remd_t(i),i=1,nrep)
288 if (index(controlcard,'MLIST').gt.0) then
290 call card_concat(controlcard1)
291 read(controlcard1,*) (remd_m(i),i=1,nrep)
292 if(me.eq.king.or..not.out1file) then
293 write (iout,*)'mlist',(remd_m(i),i=1,nrep)
296 iremd_m_total=iremd_m_total+remd_m(i)
298 write (iout,*) 'Total number of replicas ',iremd_m_total
301 if(me.eq.king.or..not.out1file)
302 & write (iout,'(/30(1h=),a,29(1h=)/)') " End of REMD run setup "
305 c--------------------------------------------------------------------------
306 subroutine read_MDpar
310 implicit real*8 (a-h,o-z)
312 include 'COMMON.IOUNITS'
313 include 'COMMON.TIME1'
316 include 'COMMON.LANGEVIN'
318 include 'COMMON.LANGEVIN.lang0'
320 include 'COMMON.INTERACT'
321 include 'COMMON.NAMES'
323 include 'COMMON.SETUP'
324 include 'COMMON.CONTROL'
325 include 'COMMON.SPLITELE'
327 character*320 controlcard
329 call card_concat(controlcard)
330 call readi(controlcard,"NSTEP",n_timestep,1000000)
331 call readi(controlcard,"NTWE",ntwe,100)
332 call readi(controlcard,"NTWX",ntwx,1000)
333 call reada(controlcard,"DT",d_time,1.0d-1)
334 call reada(controlcard,"DVMAX",dvmax,2.0d1)
335 call reada(controlcard,"DAMAX",damax,1.0d1)
336 call reada(controlcard,"EDRIFTMAX",edriftmax,1.0d+1)
337 call readi(controlcard,"LANG",lang,0)
338 RESPA = index(controlcard,"RESPA") .gt. 0
339 call readi(controlcard,"NTIME_SPLIT",ntime_split,1)
340 ntime_split0=ntime_split
341 call readi(controlcard,"MAXTIME_SPLIT",maxtime_split,64)
342 ntime_split0=ntime_split
343 call reada(controlcard,"R_CUT",r_cut,2.0d0)
344 call reada(controlcard,"LAMBDA",rlamb,0.3d0)
345 rest = index(controlcard,"REST").gt.0
346 tbf = index(controlcard,"TBF").gt.0
347 usampl = index(controlcard,"USAMPL").gt.0
348 mdpdb = index(controlcard,"MDPDB").gt.0
349 call reada(controlcard,"T_BATH",t_bath,300.0d0)
350 call reada(controlcard,"TAU_BATH",tau_bath,1.0d-1)
351 call reada(controlcard,"EQ_TIME",eq_time,1.0d+4)
352 call readi(controlcard,"RESET_MOMENT",count_reset_moment,1000)
353 if (count_reset_moment.eq.0) count_reset_moment=1000000000
354 call readi(controlcard,"RESET_VEL",count_reset_vel,1000)
355 reset_moment=lang.eq.0 .and. tbf .and. count_reset_moment.gt.0
356 reset_vel=lang.eq.0 .and. tbf .and. count_reset_vel.gt.0
357 if (count_reset_vel.eq.0) count_reset_vel=1000000000
358 large = index(controlcard,"LARGE").gt.0
359 print_compon = index(controlcard,"PRINT_COMPON").gt.0
360 rattle = index(controlcard,"RATTLE").gt.0
361 c if performing umbrella sampling, fragments constrained are read from the fragment file
367 if(me.eq.king.or..not.out1file) then
369 write (iout,'(27(1h=),a26,27(1h=))') " Parameters of the MD run "
371 write (iout,'(a)') "The units are:"
372 write (iout,'(a)') "positions: angstrom, time: 48.9 fs"
373 write (iout,'(2a)') "velocity: angstrom/(48.9 fs),",
374 & " acceleration: angstrom/(48.9 fs)**2"
375 write (iout,'(a)') "energy: kcal/mol, temperature: K"
377 write (iout,'(a60,i10)') "Number of time steps:",n_timestep
378 write (iout,'(a60,f10.5,a)')
379 & "Initial time step of numerical integration:",d_time,
381 write (iout,'(60x,f10.5,a)') d_time*48.9," fs"
383 write (iout,'(2a,i4,a)')
384 & "A-MTS algorithm used; initial time step for fast-varying",
385 & " short-range forces split into",ntime_split," steps."
386 write (iout,'(a,f5.2,a,f5.2)') "Short-range force cutoff",
387 & r_cut," lambda",rlamb
389 write (iout,'(2a,f10.5)')
390 & "Maximum acceleration threshold to reduce the time step",
391 & "/increase split number:",damax
392 write (iout,'(2a,f10.5)')
393 & "Maximum predicted energy drift to reduce the timestep",
394 & "/increase split number:",edriftmax
395 write (iout,'(a60,f10.5)')
396 & "Maximum velocity threshold to reduce velocities:",dvmax
397 write (iout,'(a60,i10)') "Frequency of property output:",ntwe
398 write (iout,'(a60,i10)') "Frequency of coordinate output:",ntwx
399 if (rattle) write (iout,'(a60)')
400 & "Rattle algorithm used to constrain the virtual bonds"
404 call reada(controlcard,"ETAWAT",etawat,0.8904d0)
405 call reada(controlcard,"RWAT",rwat,1.4d0)
406 call reada(controlcard,"SCAL_FRIC",scal_fric,2.0d-2)
407 surfarea=index(controlcard,"SURFAREA").gt.0
408 call readi(controlcard,"RESET_FRICMAT",reset_fricmat,1000)
409 if(me.eq.king.or..not.out1file)then
410 write (iout,'(/a,$)') "Langevin dynamics calculation"
413 & " with direct integration of Langevin equations"
414 else if (lang.eq.2) then
415 write (iout,'(a/)') " with TINKER stochasic MD integrator"
416 else if (lang.eq.3) then
417 write (iout,'(a/)') " with Ciccotti's stochasic MD integrator"
418 else if (lang.eq.4) then
419 write (iout,'(a/)') " in overdamped mode"
421 write (iout,'(//a,i5)')
422 & "=========== ERROR: Unknown Langevin dynamics mode:",lang
425 write (iout,'(a60,f10.5)') "Temperature:",t_bath
426 write (iout,'(a60,f10.5)') "Viscosity of the solvent:",etawat
427 write (iout,'(a60,f10.5)') "Radius of solvent molecule:",rwat
428 write (iout,'(a60,f10.5)')
429 & "Scaling factor of the friction forces:",scal_fric
430 if (surfarea) write (iout,'(2a,i10,a)')
431 & "Friction coefficients will be scaled by solvent-accessible",
432 & " surface area every",reset_fricmat," steps."
434 c Calculate friction coefficients and bounds of stochastic forces
435 eta=6*pi*cPoise*etawat
436 if(me.eq.king.or..not.out1file)
437 & write(iout,'(a60,f10.5)')"Eta of the solvent in natural units:"
439 gamp=scal_fric*(pstok+rwat)*eta
440 stdfp=dsqrt(2*Rb*t_bath/d_time)
442 gamsc(i)=scal_fric*(restok(i)+rwat)*eta
443 stdfsc(i)=dsqrt(2*Rb*t_bath/d_time)
445 if(me.eq.king.or..not.out1file)then
446 write (iout,'(/2a/)')
447 & "Radii of site types and friction coefficients and std's of",
448 & " stochastic forces of fully exposed sites"
449 write (iout,'(a5,f5.2,2f10.5)')'p',pstok,gamp,stdfp*dsqrt(gamp)
451 write (iout,'(a5,f5.2,2f10.5)') restyp(i),restok(i),
452 & gamsc(i),stdfsc(i)*dsqrt(gamsc(i))
456 if(me.eq.king.or..not.out1file)then
457 write (iout,'(a)') "Berendsen bath calculation"
458 write (iout,'(a60,f10.5)') "Temperature:",t_bath
459 write (iout,'(a60,f10.5)') "Coupling constant (tau):",tau_bath
461 & write (iout,'(a,i10,a)') "Momenta will be reset at zero every",
462 & count_reset_moment," steps"
464 & write (iout,'(a,i10,a)')
465 & "Velocities will be reset at random every",count_reset_vel,
469 if(me.eq.king.or..not.out1file)
470 & write (iout,'(a31)') "Microcanonical mode calculation"
472 if(me.eq.king.or..not.out1file)then
473 if (rest) write (iout,'(/a/)') "===== Calculation restarted ===="
475 write(iout,*) "MD running with constraints."
476 write(iout,*) "Equilibration time ", eq_time, " mtus."
477 write(iout,*) "Constraining ", nfrag," fragments."
478 write(iout,*) "Length of each fragment, weight and q0:"
480 write (iout,*) "Set of restraints #",iset
482 write(iout,'(2i5,f8.1,f7.4)') ifrag(1,i,iset),
483 & ifrag(2,i,iset),wfrag(i,iset),qinfrag(i,iset)
485 write(iout,*) "constraints between ", npair, "fragments."
486 write(iout,*) "constraint pairs, weights and q0:"
488 write(iout,'(2i5,f8.1,f7.4)') ipair(1,i,iset),
489 & ipair(2,i,iset),wpair(i,iset),qinpair(i,iset)
491 write(iout,*) "angle constraints within ", nfrag_back,
492 & "backbone fragments."
493 write(iout,*) "fragment, weights:"
495 write(iout,'(2i5,3f8.1)') ifrag_back(1,i,iset),
496 & ifrag_back(2,i,iset),wfrag_back(1,i,iset),
497 & wfrag_back(2,i,iset),wfrag_back(3,i,iset)
500 iset=mod(kolor,nset)+1
503 if(me.eq.king.or..not.out1file)
504 & write (iout,'(/30(1h=),a,29(1h=)/)') " End of MD run setup "
507 c------------------------------------------------------------------------------
510 C Read molecular data.
512 implicit real*8 (a-h,o-z)
518 include 'COMMON.IOUNITS'
521 include 'COMMON.INTERACT'
522 include 'COMMON.LOCAL'
523 include 'COMMON.NAMES'
524 include 'COMMON.CHAIN'
525 include 'COMMON.FFIELD'
526 include 'COMMON.SBRIDGE'
527 include 'COMMON.HEADER'
528 include 'COMMON.CONTROL'
529 include 'COMMON.DBASE'
530 include 'COMMON.THREAD'
531 include 'COMMON.CONTACTS'
532 include 'COMMON.TORCNSTR'
533 include 'COMMON.TIME1'
534 include 'COMMON.BOUNDS'
536 include 'COMMON.SETUP'
537 character*4 sequence(maxres)
539 double precision x(maxvar)
540 character*256 pdbfile
541 character*320 weightcard
542 character*80 weightcard_t,ucase
543 dimension itype_pdb(maxres)
544 common /pizda/ itype_pdb
545 logical seq_comp,fail
546 double precision energia(0:n_ene)
552 C Read weights of the subsequent energy terms.
553 call card_concat(weightcard)
554 call reada(weightcard,'WLONG',wlong,1.0D0)
555 call reada(weightcard,'WSC',wsc,wlong)
556 call reada(weightcard,'WSCP',wscp,wlong)
557 call reada(weightcard,'WELEC',welec,1.0D0)
558 call reada(weightcard,'WVDWPP',wvdwpp,welec)
559 call reada(weightcard,'WEL_LOC',wel_loc,1.0D0)
560 call reada(weightcard,'WCORR4',wcorr4,0.0D0)
561 call reada(weightcard,'WCORR5',wcorr5,0.0D0)
562 call reada(weightcard,'WCORR6',wcorr6,0.0D0)
563 call reada(weightcard,'WTURN3',wturn3,1.0D0)
564 call reada(weightcard,'WTURN4',wturn4,1.0D0)
565 call reada(weightcard,'WTURN6',wturn6,1.0D0)
566 call reada(weightcard,'WSCCOR',wsccor,1.0D0)
567 call reada(weightcard,'WSTRAIN',wstrain,1.0D0)
568 call reada(weightcard,'WBOND',wbond,1.0D0)
569 call reada(weightcard,'WTOR',wtor,1.0D0)
570 call reada(weightcard,'WTORD',wtor_d,1.0D0)
571 call reada(weightcard,'WANG',wang,1.0D0)
572 call reada(weightcard,'WSCLOC',wscloc,1.0D0)
573 call reada(weightcard,'SCAL14',scal14,0.4D0)
574 call reada(weightcard,'SCALSCP',scalscp,1.0d0)
575 call reada(weightcard,'CUTOFF',cutoff_corr,7.0d0)
576 call reada(weightcard,'DELT_CORR',delt_corr,0.5d0)
577 call reada(weightcard,'TEMP0',temp0,300.0d0)
578 if (index(weightcard,'SOFT').gt.0) ipot=6
579 C 12/1/95 Added weight for the multi-body term WCORR
580 call reada(weightcard,'WCORRH',wcorr,1.0D0)
581 if (wcorr4.gt.0.0d0) wcorr=wcorr4
601 if(me.eq.king.or..not.out1file)
602 & write (iout,10) wsc,wscp,welec,wvdwpp,wbond,wang,wscloc,wtor,
603 & wtor_d,wstrain,wel_loc,wcorr,wcorr5,wcorr6,wsccor,wturn3,
605 10 format (/'Energy-term weights (unscaled):'//
606 & 'WSCC= ',f10.6,' (SC-SC)'/
607 & 'WSCP= ',f10.6,' (SC-p)'/
608 & 'WELEC= ',f10.6,' (p-p electr)'/
609 & 'WVDWPP= ',f10.6,' (p-p VDW)'/
610 & 'WBOND= ',f10.6,' (stretching)'/
611 & 'WANG= ',f10.6,' (bending)'/
612 & 'WSCLOC= ',f10.6,' (SC local)'/
613 & 'WTOR= ',f10.6,' (torsional)'/
614 & 'WTORD= ',f10.6,' (double torsional)'/
615 & 'WSTRAIN=',f10.6,' (SS bridges & dist. cnstr.)'/
616 & 'WEL_LOC=',f10.6,' (multi-body 3-rd order)'/
617 & 'WCORR4= ',f10.6,' (multi-body 4th order)'/
618 & 'WCORR5= ',f10.6,' (multi-body 5th order)'/
619 & 'WCORR6= ',f10.6,' (multi-body 6th order)'/
620 & 'WSCCOR= ',f10.6,' (back-scloc correlation)'/
621 & 'WTURN3= ',f10.6,' (turns, 3rd order)'/
622 & 'WTURN4= ',f10.6,' (turns, 4th order)'/
623 & 'WTURN6= ',f10.6,' (turns, 6th order)')
624 if(me.eq.king.or..not.out1file)then
625 if (wcorr4.gt.0.0d0) then
626 write (iout,'(/2a/)') 'Local-electrostatic type correlation ',
627 & 'between contact pairs of peptide groups'
628 write (iout,'(2(a,f5.3/))')
629 & 'Cutoff on 4-6th order correlation terms: ',cutoff_corr,
630 & 'Range of quenching the correlation terms:',2*delt_corr
631 else if (wcorr.gt.0.0d0) then
632 write (iout,'(/2a/)') 'Hydrogen-bonding correlation ',
633 & 'between contact pairs of peptide groups'
635 write (iout,'(a,f8.3)')
636 & 'Scaling factor of 1,4 SC-p interactions:',scal14
637 write (iout,'(a,f8.3)')
638 & 'General scaling factor of SC-p interactions:',scalscp
640 r0_corr=cutoff_corr-delt_corr
642 aad(i,1)=scalscp*aad(i,1)
643 aad(i,2)=scalscp*aad(i,2)
644 bad(i,1)=scalscp*bad(i,1)
645 bad(i,2)=scalscp*bad(i,2)
647 call rescale_weights(t_bath)
648 if(me.eq.king.or..not.out1file)
649 & write (iout,22) wsc,wscp,welec,wvdwpp,wbond,wang,wscloc,wtor,
650 & wtor_d,wstrain,wel_loc,wcorr,wcorr5,wcorr6,wsccor,wturn3,
652 22 format (/'Energy-term weights (scaled):'//
653 & 'WSCC= ',f10.6,' (SC-SC)'/
654 & 'WSCP= ',f10.6,' (SC-p)'/
655 & 'WELEC= ',f10.6,' (p-p electr)'/
656 & 'WVDWPP= ',f10.6,' (p-p VDW)'/
657 & 'WBOND= ',f10.6,' (stretching)'/
658 & 'WANG= ',f10.6,' (bending)'/
659 & 'WSCLOC= ',f10.6,' (SC local)'/
660 & 'WTOR= ',f10.6,' (torsional)'/
661 & 'WTORD= ',f10.6,' (double torsional)'/
662 & 'WSTRAIN=',f10.6,' (SS bridges & dist. cnstr.)'/
663 & 'WEL_LOC=',f10.6,' (multi-body 3-rd order)'/
664 & 'WCORR4= ',f10.6,' (multi-body 4th order)'/
665 & 'WCORR5= ',f10.6,' (multi-body 5th order)'/
666 & 'WCORR6= ',f10.6,' (multi-body 6th order)'/
667 & 'WSCCOR= ',f10.6,' (back-scloc correlatkion)'/
668 & 'WTURN3= ',f10.6,' (turns, 3rd order)'/
669 & 'WTURN4= ',f10.6,' (turns, 4th order)'/
670 & 'WTURN6= ',f10.6,' (turns, 6th order)')
671 if(me.eq.king.or..not.out1file)
672 & write (iout,*) "Reference temperature for weights calculation:",
674 call reada(weightcard,"D0CM",d0cm,3.78d0)
675 call reada(weightcard,"AKCM",akcm,15.1d0)
676 call reada(weightcard,"AKTH",akth,11.0d0)
677 call reada(weightcard,"AKCT",akct,12.0d0)
678 call reada(weightcard,"V1SS",v1ss,-1.08d0)
679 call reada(weightcard,"V2SS",v2ss,7.61d0)
680 call reada(weightcard,"V3SS",v3ss,13.7d0)
681 call reada(weightcard,"EBR",ebr,-5.50D0)
682 dyn_ss=(index(weightcard,'DYN_SS').gt.0)
684 dyn_ss_mask(i)=.false.
688 dyn_ssbond_ij(i,j)=1.0d300
691 call reada(weightcard,"HT",Ht,0.0D0)
693 ss_depth=ebr/wsc-0.25*eps(1,1)
694 Ht=Ht/wsc-0.25*eps(1,1)
695 akcm=akcm*wstrain/wsc
696 akth=akth*wstrain/wsc
697 akct=akct*wstrain/wsc
698 v1ss=v1ss*wstrain/wsc
699 v2ss=v2ss*wstrain/wsc
700 v3ss=v3ss*wstrain/wsc
702 ss_depth=ebr/wstrain-0.25*eps(1,1)*wsc/wstrain
705 if(me.eq.king.or..not.out1file) then
706 write (iout,*) "Parameters of the SS-bond potential:"
707 write (iout,*) "D0CM",d0cm," AKCM",akcm," AKTH",akth,
709 write (iout,*) "V1SS",v1ss," V2SS",v2ss," V3SS",v3ss
710 write (iout,*) "EBR",ebr," SS_DEPTH",ss_depth
711 write (iout,*)" HT",Ht
712 c print *,'indpdb=',indpdb,' pdbref=',pdbref
714 if (indpdb.gt.0 .or. pdbref) then
715 read(inp,'(a)') pdbfile
716 if(me.eq.king.or..not.out1file)
717 & write (iout,'(2a)') 'PDB data will be read from file ',
718 & pdbfile(:ilen(pdbfile))
719 open(ipdbin,file=pdbfile,status='old',err=33)
721 33 write (iout,'(a)') 'Error opening PDB file.'
724 c print *,'Begin reading pdb data'
726 c print *,'Finished reading pdb data'
727 if(me.eq.king.or..not.out1file)
728 & write (iout,'(a,i3,a,i3)')'nsup=',nsup,
729 & ' nstart_sup=',nstart_sup
731 itype_pdb(i)=itype(i)
735 nct=nstart_sup+nsup-1
736 call contact(.false.,ncont_ref,icont_ref,co)
739 if(me.eq.king.or..not.out1file)
740 & write(iout,*)'Adding sidechains'
744 if (iti.ne.10 .and. itype(i).ne.ntyp1) then
747 do while (fail.and.nsi.le.maxsi)
748 call gen_side(iti,theta(i+1),alph(i),omeg(i),fail)
751 if(fail) write(iout,*)'Adding sidechain failed for res ',
752 & i,' after ',nsi,' trials'
757 if (indpdb.eq.0) then
758 C Read sequence if not taken from the pdb file.
760 c print *,'nres=',nres
761 if (iscode.gt.0) then
762 read (inp,'(80a1)') (sequence(i)(1:1),i=1,nres)
764 read (inp,'(20(1x,a3))') (sequence(i),i=1,nres)
766 C Convert sequence to numeric code
768 itype(i)=rescode(i,sequence(i),iscode)
770 C Assign initial virtual bond lengths
776 vbld(i+nres)=dsc(iabs(itype(i)))
777 vbld_inv(i+nres)=dsc_inv(iabs(itype(i)))
778 c write (iout,*) "i",i," itype",itype(i),
779 c & " dsc",dsc(itype(i))," vbld",vbld(i),vbld(i+nres)
783 c print '(20i4)',(itype(i),i=1,nres)
786 if (itype(i).eq.ntyp1 .or. itype(i+1).eq.ntyp1) then
788 if (itype(i).eq.ntyp1) then
792 else if (iabs(itype(i+1)).ne.20) then
794 else if (iabs(itype(i)).ne.20) then
801 if(me.eq.king.or..not.out1file)then
802 write (iout,*) "ITEL"
804 write (iout,*) i,itype(i),itel(i)
806 print *,'Call Read_Bridge.'
809 C 8/13/98 Set limits to generating the dihedral angles
814 read (inp,*) ndih_constr
815 if (ndih_constr.gt.0) then
817 read (inp,*) (idih_constr(i),phi0(i),drange(i),i=1,ndih_constr)
818 if(me.eq.king.or..not.out1file)then
820 & 'There are',ndih_constr,' constraints on phi angles.'
822 write (iout,'(i5,2f8.3)') idih_constr(i),phi0(i),drange(i)
826 phi0(i)=deg2rad*phi0(i)
827 drange(i)=deg2rad*drange(i)
829 if(me.eq.king.or..not.out1file)
830 & write (iout,*) 'FTORS',ftors
833 phibound(1,ii) = phi0(i)-drange(i)
834 phibound(2,ii) = phi0(i)+drange(i)
841 write (iout,'(a)') 'Boundaries in phi angle sampling:'
843 write (iout,'(a3,i5,2f10.1)')
844 & restyp(itype(i)),i,phibound(1,i)*rad2deg,phibound(2,i)*rad2deg
850 cd print *,'NNT=',NNT,' NCT=',NCT
851 if (itype(1).eq.ntyp1) nnt=2
852 if (itype(nres).eq.ntyp1) nct=nct-1
854 if(me.eq.king.or..not.out1file)
855 & write (iout,'(a,i3)') 'nsup=',nsup
857 if (nsup.le.(nct-nnt+1)) then
858 do i=0,nct-nnt+1-nsup
859 if (seq_comp(itype(nnt+i),itype_pdb(nstart_sup),nsup)) then
865 & 'Error - sequences to be superposed do not match.'
868 do i=0,nsup-(nct-nnt+1)
869 if (seq_comp(itype(nnt),itype_pdb(nstart_sup+i),nct-nnt+1))
871 nstart_sup=nstart_sup+i
877 & 'Error - sequences to be superposed do not match.'
880 if (nsup.eq.0) nsup=nct-nnt
881 if (nstart_sup.eq.0) nstart_sup=nnt
882 if (nstart_seq.eq.0) nstart_seq=nnt
883 if(me.eq.king.or..not.out1file)
884 & write (iout,*) 'nsup=',nsup,' nstart_sup=',nstart_sup,
885 & ' nstart_seq=',nstart_seq
887 c--- Zscore rms -------
888 if (nz_start.eq.0) nz_start=nnt
889 if (nz_end.eq.0 .and. nsup.gt.0) then
891 else if (nz_end.eq.0) then
894 if(me.eq.king.or..not.out1file)then
895 write (iout,*) 'NZ_START=',nz_start,' NZ_END=',nz_end
896 write (iout,*) 'IZ_SC=',iz_sc
898 c----------------------
901 if (.not.pdbref) then
902 call read_angles(inp,*38)
904 38 write (iout,'(a)') 'Error reading reference structure.'
906 call MPI_Finalize(MPI_COMM_WORLD,IERROR)
907 stop 'Error reading reference structure'
911 czscore call geom_to_var(nvar,coord_exp_zs(1,1))
921 call contact(.true.,ncont_ref,icont_ref,co)
923 c write (iout,*) "constr_dist",constr_dist,nstart_sup,nsup
925 if (constr_dist.gt.0) call read_dist_constr
926 write (iout,*) "After read_dist_constr nhpb",nhpb
928 if(me.eq.king.or..not.out1file)
929 & write (iout,*) 'Contact order:',co
931 if(me.eq.king.or..not.out1file)
932 & write (2,*) 'Shifting contacts:',nstart_seq,nstart_sup
935 icont_ref(j,i)=icont_ref(j,i)+nstart_seq-nstart_sup
937 if(me.eq.king.or..not.out1file)
938 & write (2,*) i,' ',restyp(itype(icont_ref(1,i))),' ',
939 & icont_ref(1,i),' ',
940 & restyp(itype(icont_ref(2,i))),' ',icont_ref(2,i)
944 if (indpdb.eq.0 .and. modecalc.ne.2 .and. modecalc.ne.4
945 & .and. modecalc.ne.8 .and. modecalc.ne.9 .and.
946 & modecalc.ne.10) then
947 C If input structure hasn't been supplied from the PDB file read or generate
949 if (iranconf.eq.0 .and. .not. extconf) then
950 if(me.eq.king.or..not.out1file .and.fg_rank.eq.0)
951 & write (iout,'(a)') 'Initial geometry will be read in.'
953 read(inp,'(8f10.5)',end=36,err=36)
954 & ((c(l,k),l=1,3),k=1,nres),
955 & ((c(l,k+nres),l=1,3),k=nnt,nct)
956 write (iout,*) "Exit READ_CART"
957 write (iout,'(8f10.5)')
958 & ((c(l,k),l=1,3),k=1,nres),
959 & ((c(l,k+nres),l=1,3),k=nnt,nct)
960 call int_from_cart1(.true.)
961 write (iout,*) "Finish INT_TO_CART"
964 dc(j,i)=c(j,i+1)-c(j,i)
965 dc_norm(j,i)=dc_norm(j,i)*vbld_inv(i+1)
969 if (itype(i).ne.10 .and. itype(i).ne.ntyp1) then
971 dc(j,i+nres)=c(j,i+nres)-c(j,i)
972 dc_norm(j,i+nres)=dc_norm(j,i+nres)*vbld_inv(i+nres)
978 call read_angles(inp,*36)
981 36 write (iout,'(a)') 'Error reading angle file.'
983 call mpi_finalize( MPI_COMM_WORLD,IERR )
985 stop 'Error reading angle file.'
987 else if (extconf) then
988 if(me.eq.king.or..not.out1file .and. fg_rank.eq.0)
989 & write (iout,'(a)') 'Extended chain initial geometry.'
991 theta(i)=90d0*deg2rad
997 alph(i)=110d0*deg2rad
1000 omeg(i)=-120d0*deg2rad
1001 if (itype(i).le.0) omeg(i)=-omeg(i)
1004 if(me.eq.king.or..not.out1file)
1005 & write (iout,'(a)') 'Random-generated initial geometry.'
1009 if (me.eq.king .or. fg_rank.eq.0 .and. (
1010 & modecalc.eq.12 .or. modecalc.eq.14) ) then
1014 call gen_rand_conf(itmp,*30)
1016 30 write (iout,*) 'Failed to generate random conformation',
1017 & ', itrial=',itrial
1018 write (*,*) 'Processor:',me,
1019 & ' Failed to generate random conformation',
1029 write (iout,'(a,i3,a)') 'Processor:',me,
1030 & ' error in generating random conformation.'
1031 write (*,'(a,i3,a)') 'Processor:',me,
1032 & ' error in generating random conformation.'
1035 call MPI_Abort(mpi_comm_world,error_msg,ierrcode)
1041 call gen_rand_conf(itmp,*30)
1043 30 write (iout,*) 'Failed to generate random conformation',
1044 & ', itrial=',itrial
1045 write (*,*) 'Failed to generate random conformation',
1046 & ', itrial=',itrial
1048 write (iout,'(a,i3,a)') 'Processor:',me,
1049 & ' error in generating random conformation.'
1050 write (*,'(a,i3,a)') 'Processor:',me,
1051 & ' error in generating random conformation.'
1056 elseif (modecalc.eq.4) then
1057 read (inp,'(a)') intinname
1058 open (intin,file=intinname,status='old',err=333)
1059 if (me.eq.king .or. .not.out1file.and.fg_rank.eq.0)
1060 & write (iout,'(a)') 'intinname',intinname
1061 write (*,'(a)') 'Processor',myrank,' intinname',intinname
1063 333 write (iout,'(2a)') 'Error opening angle file ',intinname
1065 call MPI_Finalize(MPI_COMM_WORLD,IERR)
1067 stop 'Error opening angle file.'
1071 C Generate distance constraints, if the PDB structure is to be regularized.
1072 if (nthread.gt.0) then
1073 call read_threadbase
1076 if (me.eq.king .or. .not. out1file)
1078 if (ns.gt.0 .and. (me.eq.king .or. .not.out1file) ) then
1079 write (iout,'(/a,i3,a)')
1080 & 'The chain contains',ns,' disulfide-bridging cysteines.'
1081 write (iout,'(20i4)') (iss(i),i=1,ns)
1083 write(iout,*)"Running with dynamic disulfide-bond formation"
1085 write (iout,'(/a/)') 'Pre-formed links are:'
1091 write (iout,'(2a,i3,3a,i3,a,3f10.3)')
1092 & restyp(it1),'(',i1,') -- ',restyp(it2),'(',i2,')',dhpb(i),
1098 if (ns.gt.0.and.dyn_ss) then
1102 forcon(i-nss)=forcon(i)
1109 dyn_ss_mask(iss(i))=.true.
1112 if (i2ndstr.gt.0) call secstrp2dihc
1113 c call geom_to_var(nvar,x)
1114 c call etotal(energia(0))
1115 c call enerprint(energia(0))
1116 c call briefout(0,etot)
1118 cd write (iout,'(2(a,i3))') 'NNT',NNT,' NCT',NCT
1119 cd write (iout,'(a)') 'Variable list:'
1120 cd write (iout,'(i4,f10.5)') (i,rad2deg*x(i),i=1,nvar)
1122 if (me.eq.king .or. (fg_rank.eq.0 .and. .not.out1file))
1123 & write (iout,'(//80(1h*)/20x,a,i4,a/80(1h*)//)')
1124 & 'Processor',myrank,': end reading molecular data.'
1128 c--------------------------------------------------------------------------
1129 logical function seq_comp(itypea,itypeb,length)
1131 integer length,itypea(length),itypeb(length)
1134 if (itypea(i).ne.itypeb(i)) then
1142 c-----------------------------------------------------------------------------
1143 subroutine read_bridge
1144 C Read information about disulfide bridges.
1145 implicit real*8 (a-h,o-z)
1146 include 'DIMENSIONS'
1150 include 'COMMON.IOUNITS'
1151 include 'COMMON.GEO'
1152 include 'COMMON.VAR'
1153 include 'COMMON.INTERACT'
1154 include 'COMMON.LOCAL'
1155 include 'COMMON.NAMES'
1156 include 'COMMON.CHAIN'
1157 include 'COMMON.FFIELD'
1158 include 'COMMON.SBRIDGE'
1159 include 'COMMON.HEADER'
1160 include 'COMMON.CONTROL'
1161 include 'COMMON.DBASE'
1162 include 'COMMON.THREAD'
1163 include 'COMMON.TIME1'
1164 include 'COMMON.SETUP'
1165 C Read bridging residues.
1166 read (inp,*) ns,(iss(i),i=1,ns)
1168 if(me.eq.king.or..not.out1file)
1169 & write (iout,*) 'ns=',ns,' iss:',(iss(i),i=1,ns)
1170 C Check whether the specified bridging residues are cystines.
1172 if (itype(iss(i)).ne.1) then
1173 if (me.eq.king.or..not.out1file) write (iout,'(2a,i3,a)')
1174 & 'Do you REALLY think that the residue ',
1175 & restyp(itype(iss(i))),i,
1176 & ' can form a disulfide bridge?!!!'
1177 write (*,'(2a,i3,a)')
1178 & 'Do you REALLY think that the residue ',
1179 & restyp(itype(iss(i))),i,
1180 & ' can form a disulfide bridge?!!!'
1182 call MPI_Finalize(MPI_COMM_WORLD,ierror)
1187 C Read preformed bridges.
1189 read (inp,*) nss,(ihpb(i),jhpb(i),i=1,nss)
1191 &write (iout,*) 'nss=',nss,' ihpb,jhpb: ',(ihpb(i),jhpb(i),i=1,nss)
1194 C Check if the residues involved in bridges are in the specified list of
1195 C bridging residues.
1198 if (ihpb(i).eq.ihpb(j).or.ihpb(i).eq.jhpb(j)
1199 & .or.jhpb(i).eq.ihpb(j).or.jhpb(i).eq.jhpb(j)) then
1200 write (iout,'(a,i3,a)') 'Disulfide pair',i,
1201 & ' contains residues present in other pairs.'
1202 write (*,'(a,i3,a)') 'Disulfide pair',i,
1203 & ' contains residues present in other pairs.'
1205 call MPI_Finalize(MPI_COMM_WORLD,ierror)
1211 if (ihpb(i).eq.iss(j)) goto 10
1213 write (iout,'(a,i3,a)') 'Pair',i,' contains unknown cystine.'
1216 if (jhpb(i).eq.iss(j)) goto 20
1218 write (iout,'(a,i3,a)') 'Pair',i,' contains unknown cystine.'
1224 ihpb(i)=ihpb(i)+nres
1225 jhpb(i)=jhpb(i)+nres
1231 c----------------------------------------------------------------------------
1232 subroutine read_x(kanal,*)
1233 implicit real*8 (a-h,o-z)
1234 include 'DIMENSIONS'
1235 include 'COMMON.GEO'
1236 include 'COMMON.VAR'
1237 include 'COMMON.CHAIN'
1238 include 'COMMON.IOUNITS'
1239 include 'COMMON.CONTROL'
1240 include 'COMMON.LOCAL'
1241 include 'COMMON.INTERACT'
1242 c Read coordinates from input
1244 read(kanal,'(8f10.5)',end=10,err=10)
1245 & ((c(l,k),l=1,3),k=1,nres),
1246 & ((c(l,k+nres),l=1,3),k=nnt,nct)
1249 c(j,2*nres)=c(j,nres)
1251 call int_from_cart1(.false.)
1254 dc(j,i)=c(j,i+1)-c(j,i)
1255 dc_norm(j,i)=dc(j,i)*vbld_inv(i+1)
1259 if (itype(i).ne.10 .and. itype(i).ne.ntyp1) then
1261 dc(j,i+nres)=c(j,i+nres)-c(j,i)
1262 dc_norm(j,i+nres)=dc(j,i+nres)*vbld_inv(i+nres)
1270 c----------------------------------------------------------------------------
1271 subroutine read_threadbase
1272 implicit real*8 (a-h,o-z)
1273 include 'DIMENSIONS'
1274 include 'COMMON.IOUNITS'
1275 include 'COMMON.GEO'
1276 include 'COMMON.VAR'
1277 include 'COMMON.INTERACT'
1278 include 'COMMON.LOCAL'
1279 include 'COMMON.NAMES'
1280 include 'COMMON.CHAIN'
1281 include 'COMMON.FFIELD'
1282 include 'COMMON.SBRIDGE'
1283 include 'COMMON.HEADER'
1284 include 'COMMON.CONTROL'
1285 include 'COMMON.DBASE'
1286 include 'COMMON.THREAD'
1287 include 'COMMON.TIME1'
1288 C Read pattern database for threading.
1289 read (icbase,*) nseq
1291 read (icbase,'(i5,2x,a8,2i4)') nres_base(1,i),str_nam(i),
1292 & nres_base(2,i),nres_base(3,i)
1293 read (icbase,'(9f8.3)') ((cart_base(k,j,i),k=1,3),j=1,
1295 c write (iout,'(i5,2x,a8,2i4)') nres_base(1,i),str_nam(i),
1296 c & nres_base(2,i),nres_base(3,i)
1297 c write (iout,'(9f8.3)') ((cart_base(k,j,i),k=1,3),j=1,
1301 if (weidis.eq.0.0D0) weidis=0.1D0
1310 read (inp,*) nexcl,(iexam(1,i),iexam(2,i),i=1,nexcl)
1311 write (iout,'(a,i5)') 'nexcl: ',nexcl
1312 write (iout,'(2i5)') (iexam(1,i),iexam(2,i),i=1,nexcl)
1315 c------------------------------------------------------------------------------
1316 subroutine setup_var
1317 implicit real*8 (a-h,o-z)
1318 include 'DIMENSIONS'
1319 include 'COMMON.IOUNITS'
1320 include 'COMMON.GEO'
1321 include 'COMMON.VAR'
1322 include 'COMMON.INTERACT'
1323 include 'COMMON.LOCAL'
1324 include 'COMMON.NAMES'
1325 include 'COMMON.CHAIN'
1326 include 'COMMON.FFIELD'
1327 include 'COMMON.SBRIDGE'
1328 include 'COMMON.HEADER'
1329 include 'COMMON.CONTROL'
1330 include 'COMMON.DBASE'
1331 include 'COMMON.THREAD'
1332 include 'COMMON.TIME1'
1333 C Set up variable list.
1339 if (itype(i).ne.10 .and. itype(i).ne.ntyp1) then
1341 ialph(i,1)=nvar+nside
1345 if (indphi.gt.0) then
1347 else if (indback.gt.0) then
1352 cd write (iout,'(3i4)') (i,ialph(i,1),ialph(i,2),i=2,nres-1)
1355 c----------------------------------------------------------------------------
1356 subroutine gen_dist_constr
1357 C Generate CA distance constraints.
1358 implicit real*8 (a-h,o-z)
1359 include 'DIMENSIONS'
1360 include 'COMMON.IOUNITS'
1361 include 'COMMON.GEO'
1362 include 'COMMON.VAR'
1363 include 'COMMON.INTERACT'
1364 include 'COMMON.LOCAL'
1365 include 'COMMON.NAMES'
1366 include 'COMMON.CHAIN'
1367 include 'COMMON.FFIELD'
1368 include 'COMMON.SBRIDGE'
1369 include 'COMMON.HEADER'
1370 include 'COMMON.CONTROL'
1371 include 'COMMON.DBASE'
1372 include 'COMMON.THREAD'
1373 include 'COMMON.TIME1'
1374 dimension itype_pdb(maxres)
1375 common /pizda/ itype_pdb
1377 cd print *,'gen_dist_constr: nnt=',nnt,' nct=',nct
1378 cd write (2,*) 'gen_dist_constr: nnt=',nnt,' nct=',nct,
1379 cd & ' nstart_sup',nstart_sup,' nstart_seq',nstart_seq,
1381 do i=nstart_sup,nstart_sup+nsup-1
1382 cd write (2,*) 'i',i,' seq ',restyp(itype(i+nstart_seq-nstart_sup)),
1383 cd & ' seq_pdb', restyp(itype_pdb(i))
1384 do j=i+2,nstart_sup+nsup-1
1386 ihpb(nhpb)=i+nstart_seq-nstart_sup
1387 jhpb(nhpb)=j+nstart_seq-nstart_sup
1389 dhpb(nhpb)=dist(i,j)
1392 cd write (iout,'(a)') 'Distance constraints:'
1397 cd if (ii.gt.nres) then
1402 cd write (iout,'(a,1x,a,i4,3x,a,1x,a,i4,2f10.3)')
1403 cd & restyp(itype(ii)),iden,ii,restyp(itype(jj)),iden,jj,
1404 cd & dhpb(i),forcon(i)
1408 c----------------------------------------------------------------------------
1410 implicit real*8 (a-h,o-z)
1411 include 'DIMENSIONS'
1412 include 'COMMON.MAP'
1413 include 'COMMON.IOUNITS'
1414 character*3 angid(4) /'THE','PHI','ALP','OME'/
1415 character*80 mapcard,ucase
1417 read (inp,'(a)') mapcard
1418 mapcard=ucase(mapcard)
1419 if (index(mapcard,'PHI').gt.0) then
1421 else if (index(mapcard,'THE').gt.0) then
1423 else if (index(mapcard,'ALP').gt.0) then
1425 else if (index(mapcard,'OME').gt.0) then
1428 write(iout,'(a)')'Error - illegal variable spec in MAP card.'
1429 stop 'Error - illegal variable spec in MAP card.'
1431 call readi (mapcard,'RES1',res1(imap),0)
1432 call readi (mapcard,'RES2',res2(imap),0)
1433 if (res1(imap).eq.0) then
1434 res1(imap)=res2(imap)
1435 else if (res2(imap).eq.0) then
1436 res2(imap)=res1(imap)
1438 if(res1(imap)*res2(imap).eq.0 .or. res1(imap).gt.res2(imap))then
1440 & 'Error - illegal definition of variable group in MAP.'
1441 stop 'Error - illegal definition of variable group in MAP.'
1443 call reada(mapcard,'FROM',ang_from(imap),0.0D0)
1444 call reada(mapcard,'TO',ang_to(imap),0.0D0)
1445 call readi(mapcard,'NSTEP',nstep(imap),0)
1446 if (ang_from(imap).eq.ang_to(imap) .or. nstep(imap).eq.0) then
1448 & 'Illegal boundary and/or step size specification in MAP.'
1449 stop 'Illegal boundary and/or step size specification in MAP.'
1454 c----------------------------------------------------------------------------
1456 implicit real*8 (a-h,o-z)
1457 include 'DIMENSIONS'
1458 include 'COMMON.IOUNITS'
1459 include 'COMMON.GEO'
1460 include 'COMMON.CSA'
1461 include 'COMMON.BANK'
1462 include 'COMMON.CONTROL'
1464 character*620 mcmcard
1465 call card_concat(mcmcard)
1467 call readi(mcmcard,'NCONF',nconf,50)
1468 call readi(mcmcard,'NADD',nadd,0)
1469 call readi(mcmcard,'JSTART',jstart,1)
1470 call readi(mcmcard,'JEND',jend,1)
1471 call readi(mcmcard,'NSTMAX',nstmax,500000)
1472 call readi(mcmcard,'N0',n0,1)
1473 call readi(mcmcard,'N1',n1,6)
1474 call readi(mcmcard,'N2',n2,4)
1475 call readi(mcmcard,'N3',n3,0)
1476 call readi(mcmcard,'N4',n4,0)
1477 call readi(mcmcard,'N5',n5,0)
1478 call readi(mcmcard,'N6',n6,10)
1479 call readi(mcmcard,'N7',n7,0)
1480 call readi(mcmcard,'N8',n8,0)
1481 call readi(mcmcard,'N9',n9,0)
1482 call readi(mcmcard,'N14',n14,0)
1483 call readi(mcmcard,'N15',n15,0)
1484 call readi(mcmcard,'N16',n16,0)
1485 call readi(mcmcard,'N17',n17,0)
1486 call readi(mcmcard,'N18',n18,0)
1488 vdisulf=(index(mcmcard,'DYNSS').gt.0)
1490 call readi(mcmcard,'NDIFF',ndiff,2)
1491 call reada(mcmcard,'DIFFCUT',diffcut,0.0d0)
1492 call readi(mcmcard,'IS1',is1,1)
1493 call readi(mcmcard,'IS2',is2,8)
1494 call readi(mcmcard,'NRAN0',nran0,4)
1495 call readi(mcmcard,'NRAN1',nran1,2)
1496 call readi(mcmcard,'IRR',irr,1)
1497 call readi(mcmcard,'NSEED',nseed,20)
1498 call readi(mcmcard,'NTOTAL',ntotal,10000)
1499 call reada(mcmcard,'CUT1',cut1,2.0d0)
1500 call reada(mcmcard,'CUT2',cut2,5.0d0)
1501 call reada(mcmcard,'ESTOP',estop,-3000.0d0)
1502 call readi(mcmcard,'ICMAX',icmax,3)
1503 call readi(mcmcard,'IRESTART',irestart,0)
1504 c!bankt call readi(mcmcard,'NBANKTM',ntbankm,0)
1507 call reada(mcmcard,'DELE',dele,20.0d0)
1508 call reada(mcmcard,'DIFCUT',difcut,720.0d0)
1509 call readi(mcmcard,'IREF',iref,0)
1510 call reada(mcmcard,'RMSCUT',rmscut,4.0d0)
1511 call reada(mcmcard,'PNCCUT',pnccut,0.5d0)
1512 call readi(mcmcard,'NCONF_IN',nconf_in,0)
1513 call reada(mcmcard,'RDIH_BIAS',rdih_bias,0.5d0)
1514 write (iout,*) "NCONF_IN",nconf_in
1517 c----------------------------------------------------------------------------
1518 cfmc subroutine mcmfread
1519 cfmc implicit real*8 (a-h,o-z)
1520 cfmc include 'DIMENSIONS'
1521 cfmc include 'COMMON.MCMF'
1522 cfmc include 'COMMON.IOUNITS'
1523 cfmc include 'COMMON.GEO'
1524 cfmc character*80 ucase
1525 cfmc character*620 mcmcard
1526 cfmc call card_concat(mcmcard)
1528 cfmc call readi(mcmcard,'MAXRANT',maxrant,1000)
1529 cfmc write(iout,*)'MAXRANT=',maxrant
1530 cfmc call readi(mcmcard,'MAXFAM',maxfam,maxfam_p)
1531 cfmc write(iout,*)'MAXFAM=',maxfam
1532 cfmc call readi(mcmcard,'NNET1',nnet1,5)
1533 cfmc write(iout,*)'NNET1=',nnet1
1534 cfmc call readi(mcmcard,'NNET2',nnet2,4)
1535 cfmc write(iout,*)'NNET2=',nnet2
1536 cfmc call readi(mcmcard,'NNET3',nnet3,4)
1537 cfmc write(iout,*)'NNET3=',nnet3
1538 cfmc call readi(mcmcard,'ILASTT',ilastt,0)
1539 cfmc write(iout,*)'ILASTT=',ilastt
1540 cfmc call readi(mcmcard,'MAXSTR',maxstr,maxstr_mcmf)
1541 cfmc write(iout,*)'MAXSTR=',maxstr
1542 cfmc maxstr_f=maxstr/maxfam
1543 cfmc write(iout,*)'MAXSTR_F=',maxstr_f
1544 cfmc call readi(mcmcard,'NMCMF',nmcmf,10)
1545 cfmc write(iout,*)'NMCMF=',nmcmf
1546 cfmc call readi(mcmcard,'IFOCUS',ifocus,nmcmf)
1547 cfmc write(iout,*)'IFOCUS=',ifocus
1548 cfmc call readi(mcmcard,'NLOCMCMF',nlocmcmf,1000)
1549 cfmc write(iout,*)'NLOCMCMF=',nlocmcmf
1550 cfmc call readi(mcmcard,'INTPRT',intprt,1000)
1551 cfmc write(iout,*)'INTPRT=',intprt
1552 cfmc call readi(mcmcard,'IPRT',iprt,100)
1553 cfmc write(iout,*)'IPRT=',iprt
1554 cfmc call readi(mcmcard,'IMAXTR',imaxtr,100)
1555 cfmc write(iout,*)'IMAXTR=',imaxtr
1556 cfmc call readi(mcmcard,'MAXEVEN',maxeven,1000)
1557 cfmc write(iout,*)'MAXEVEN=',maxeven
1558 cfmc call readi(mcmcard,'MAXEVEN1',maxeven1,3)
1559 cfmc write(iout,*)'MAXEVEN1=',maxeven1
1560 cfmc call readi(mcmcard,'INIMIN',inimin,200)
1561 cfmc write(iout,*)'INIMIN=',inimin
1562 cfmc call readi(mcmcard,'NSTEPMCMF',nstepmcmf,10)
1563 cfmc write(iout,*)'NSTEPMCMF=',nstepmcmf
1564 cfmc call readi(mcmcard,'NTHREAD',nthread,5)
1565 cfmc write(iout,*)'NTHREAD=',nthread
1566 cfmc call readi(mcmcard,'MAXSTEPMCMF',maxstepmcmf,2500)
1567 cfmc write(iout,*)'MAXSTEPMCMF=',maxstepmcmf
1568 cfmc call readi(mcmcard,'MAXPERT',maxpert,9)
1569 cfmc write(iout,*)'MAXPERT=',maxpert
1570 cfmc call readi(mcmcard,'IRMSD',irmsd,1)
1571 cfmc write(iout,*)'IRMSD=',irmsd
1572 cfmc call reada(mcmcard,'DENEMIN',denemin,0.01D0)
1573 cfmc write(iout,*)'DENEMIN=',denemin
1574 cfmc call reada(mcmcard,'RCUT1S',rcut1s,3.5D0)
1575 cfmc write(iout,*)'RCUT1S=',rcut1s
1576 cfmc call reada(mcmcard,'RCUT1E',rcut1e,2.0D0)
1577 cfmc write(iout,*)'RCUT1E=',rcut1e
1578 cfmc call reada(mcmcard,'RCUT2S',rcut2s,0.5D0)
1579 cfmc write(iout,*)'RCUT2S=',rcut2s
1580 cfmc call reada(mcmcard,'RCUT2E',rcut2e,0.1D0)
1581 cfmc write(iout,*)'RCUT2E=',rcut2e
1582 cfmc call reada(mcmcard,'DPERT1',d_pert1,180.0D0)
1583 cfmc write(iout,*)'DPERT1=',d_pert1
1584 cfmc call reada(mcmcard,'DPERT1A',d_pert1a,180.0D0)
1585 cfmc write(iout,*)'DPERT1A=',d_pert1a
1586 cfmc call reada(mcmcard,'DPERT2',d_pert2,90.0D0)
1587 cfmc write(iout,*)'DPERT2=',d_pert2
1588 cfmc call reada(mcmcard,'DPERT2A',d_pert2a,45.0D0)
1589 cfmc write(iout,*)'DPERT2A=',d_pert2a
1590 cfmc call reada(mcmcard,'DPERT2B',d_pert2b,90.0D0)
1591 cfmc write(iout,*)'DPERT2B=',d_pert2b
1592 cfmc call reada(mcmcard,'DPERT2C',d_pert2c,60.0D0)
1593 cfmc write(iout,*)'DPERT2C=',d_pert2c
1594 cfmc d_pert1=deg2rad*d_pert1
1595 cfmc d_pert1a=deg2rad*d_pert1a
1596 cfmc d_pert2=deg2rad*d_pert2
1597 cfmc d_pert2a=deg2rad*d_pert2a
1598 cfmc d_pert2b=deg2rad*d_pert2b
1599 cfmc d_pert2c=deg2rad*d_pert2c
1600 cfmc call reada(mcmcard,'KT_MCMF1',kt_mcmf1,1.0D0)
1601 cfmc write(iout,*)'KT_MCMF1=',kt_mcmf1
1602 cfmc call reada(mcmcard,'KT_MCMF2',kt_mcmf2,1.0D0)
1603 cfmc write(iout,*)'KT_MCMF2=',kt_mcmf2
1604 cfmc call reada(mcmcard,'DKT_MCMF1',dkt_mcmf1,10.0D0)
1605 cfmc write(iout,*)'DKT_MCMF1=',dkt_mcmf1
1606 cfmc call reada(mcmcard,'DKT_MCMF2',dkt_mcmf2,1.0D0)
1607 cfmc write(iout,*)'DKT_MCMF2=',dkt_mcmf2
1608 cfmc call reada(mcmcard,'RCUTINI',rcutini,3.5D0)
1609 cfmc write(iout,*)'RCUTINI=',rcutini
1610 cfmc call reada(mcmcard,'GRAT',grat,0.5D0)
1611 cfmc write(iout,*)'GRAT=',grat
1612 cfmc call reada(mcmcard,'BIAS_MCMF',bias_mcmf,0.0D0)
1613 cfmc write(iout,*)'BIAS_MCMF=',bias_mcmf
1617 c----------------------------------------------------------------------------
1619 implicit real*8 (a-h,o-z)
1620 include 'DIMENSIONS'
1621 include 'COMMON.MCM'
1622 include 'COMMON.MCE'
1623 include 'COMMON.IOUNITS'
1625 character*320 mcmcard
1626 call card_concat(mcmcard)
1627 call readi(mcmcard,'MAXACC',maxacc,100)
1628 call readi(mcmcard,'MAX_MCM_IT',max_mcm_it,10000)
1629 call readi(mcmcard,'MAXTRIAL',maxtrial,100)
1630 call readi(mcmcard,'MAXTRIAL_ITER',maxtrial_iter,1000)
1631 call readi(mcmcard,'MAXREPM',maxrepm,200)
1632 call reada(mcmcard,'RANFRACT',RanFract,0.5D0)
1633 call reada(mcmcard,'POOL_FRACT',pool_fraction,0.01D0)
1634 call reada(mcmcard,'OVERLAP',overlap_cut,1.0D3)
1635 call reada(mcmcard,'E_UP',e_up,5.0D0)
1636 call reada(mcmcard,'DELTE',delte,0.1D0)
1637 call readi(mcmcard,'NSWEEP',nsweep,5)
1638 call readi(mcmcard,'NSTEPH',nsteph,0)
1639 call readi(mcmcard,'NSTEPC',nstepc,0)
1640 call reada(mcmcard,'TMIN',tmin,298.0D0)
1641 call reada(mcmcard,'TMAX',tmax,298.0D0)
1642 call readi(mcmcard,'NWINDOW',nwindow,0)
1643 call readi(mcmcard,'PRINT_MC',print_mc,0)
1644 print_stat=(index(mcmcard,'NO_PRINT_STAT').le.0)
1645 print_int=(index(mcmcard,'NO_PRINT_INT').le.0)
1646 ent_read=(index(mcmcard,'ENT_READ').gt.0)
1647 call readi(mcmcard,'SAVE_FREQ',save_frequency,1000)
1648 call readi(mcmcard,'MESSAGE_FREQ',message_frequency,1000)
1649 call readi(mcmcard,'POOL_READ_FREQ',pool_read_freq,5000)
1650 call readi(mcmcard,'POOL_SAVE_FREQ',pool_save_freq,1000)
1651 call readi(mcmcard,'PRINT_FREQ',print_freq,1000)
1652 if (nwindow.gt.0) then
1653 read (inp,*) (winstart(i),winend(i),i=1,nwindow)
1655 winlen(i)=winend(i)-winstart(i)+1
1658 if (tmax.lt.tmin) tmax=tmin
1659 if (tmax.eq.tmin) then
1663 if (nstepc.gt.0 .and. nsteph.gt.0) then
1664 tsteph=(tmax/tmin)**(1.0D0/(nsteph+0.0D0))
1665 tstepc=(tmax/tmin)**(1.0D0/(nstepc+0.0D0))
1667 C Probabilities of different move types
1668 sumpro_type(0)=0.0D0
1669 call reada(mcmcard,'MULTI_BOND',sumpro_type(1),1.0d0)
1670 call reada(mcmcard,'ONE_ANGLE' ,sumpro_type(2),2.0d0)
1671 sumpro_type(2)=sumpro_type(1)+sumpro_type(2)
1672 call reada(mcmcard,'THETA' ,sumpro_type(3),0.0d0)
1673 sumpro_type(3)=sumpro_type(2)+sumpro_type(3)
1674 call reada(mcmcard,'SIDE_CHAIN',sumpro_type(4),0.5d0)
1675 sumpro_type(4)=sumpro_type(3)+sumpro_type(4)
1677 print *,'i',i,' sumprotype',sumpro_type(i)
1678 sumpro_type(i)=sumpro_type(i)/sumpro_type(MaxMoveType)
1679 print *,'i',i,' sumprotype',sumpro_type(i)
1683 c----------------------------------------------------------------------------
1684 subroutine read_minim
1685 implicit real*8 (a-h,o-z)
1686 include 'DIMENSIONS'
1687 include 'COMMON.MINIM'
1688 include 'COMMON.IOUNITS'
1690 character*320 minimcard
1691 call card_concat(minimcard)
1692 call readi(minimcard,'MAXMIN',maxmin,2000)
1693 call readi(minimcard,'MAXFUN',maxfun,5000)
1694 call readi(minimcard,'MINMIN',minmin,maxmin)
1695 call readi(minimcard,'MINFUN',minfun,maxmin)
1696 call reada(minimcard,'TOLF',tolf,1.0D-2)
1697 call reada(minimcard,'RTOLF',rtolf,1.0D-4)
1698 print_min_stat=min0(index(minimcard,'PRINT_MIN_STAT'),1)
1699 print_min_res=min0(index(minimcard,'PRINT_MIN_RES'),1)
1700 print_min_ini=min0(index(minimcard,'PRINT_MIN_INI'),1)
1701 write (iout,'(/80(1h*)/20x,a/80(1h*))')
1702 & 'Options in energy minimization:'
1703 write (iout,'(4(a,i5),a,1pe14.5,a,1pe14.5)')
1704 & 'MaxMin:',MaxMin,' MaxFun:',MaxFun,
1705 & 'MinMin:',MinMin,' MinFun:',MinFun,
1706 & ' TolF:',TolF,' RTolF:',RTolF
1709 c----------------------------------------------------------------------------
1710 subroutine read_angles(kanal,*)
1711 implicit real*8 (a-h,o-z)
1712 include 'DIMENSIONS'
1713 include 'COMMON.GEO'
1714 include 'COMMON.VAR'
1715 include 'COMMON.CHAIN'
1716 include 'COMMON.IOUNITS'
1717 include 'COMMON.CONTROL'
1718 c Read angles from input
1720 read (kanal,*,err=10,end=10) (theta(i),i=3,nres)
1721 read (kanal,*,err=10,end=10) (phi(i),i=4,nres)
1722 read (kanal,*,err=10,end=10) (alph(i),i=2,nres-1)
1723 read (kanal,*,err=10,end=10) (omeg(i),i=2,nres-1)
1726 c 9/7/01 avoid 180 deg valence angle
1727 if (theta(i).gt.179.99d0) theta(i)=179.99d0
1729 theta(i)=deg2rad*theta(i)
1730 phi(i)=deg2rad*phi(i)
1731 alph(i)=deg2rad*alph(i)
1732 omeg(i)=deg2rad*omeg(i)
1737 c----------------------------------------------------------------------------
1738 subroutine reada(rekord,lancuch,wartosc,default)
1740 character*(*) rekord,lancuch
1741 double precision wartosc,default
1744 iread=index(rekord,lancuch)
1745 if (iread.eq.0) then
1749 iread=iread+ilen(lancuch)+1
1750 read (rekord(iread:),*,err=10,end=10) wartosc
1755 c----------------------------------------------------------------------------
1756 subroutine readi(rekord,lancuch,wartosc,default)
1758 character*(*) rekord,lancuch
1759 integer wartosc,default
1762 iread=index(rekord,lancuch)
1763 if (iread.eq.0) then
1767 iread=iread+ilen(lancuch)+1
1768 read (rekord(iread:),*,err=10,end=10) wartosc
1773 c----------------------------------------------------------------------------
1774 subroutine multreadi(rekord,lancuch,tablica,dim,default)
1777 integer tablica(dim),default
1778 character*(*) rekord,lancuch
1785 iread=index(rekord,lancuch(:ilen(lancuch))//"=")
1786 if (iread.eq.0) return
1787 iread=iread+ilen(lancuch)+1
1788 read (rekord(iread:),*,end=10,err=10) (tablica(i),i=1,dim)
1791 c----------------------------------------------------------------------------
1792 subroutine multreada(rekord,lancuch,tablica,dim,default)
1795 double precision tablica(dim),default
1796 character*(*) rekord,lancuch
1803 iread=index(rekord,lancuch(:ilen(lancuch))//"=")
1804 if (iread.eq.0) return
1805 iread=iread+ilen(lancuch)+1
1806 read (rekord(iread:),*,end=10,err=10) (tablica(i),i=1,dim)
1809 c----------------------------------------------------------------------------
1810 subroutine openunits
1811 implicit real*8 (a-h,o-z)
1812 include 'DIMENSIONS'
1815 character*16 form,nodename
1818 include 'COMMON.SETUP'
1819 include 'COMMON.IOUNITS'
1821 include 'COMMON.CONTROL'
1822 integer lenpre,lenpot,ilen,lentmp
1824 character*3 out1file_text,ucase
1827 c print *,"Processor",myrank,"fg_rank",fg_rank," entered openunits"
1828 call getenv_loc("PREFIX",prefix)
1830 call getenv_loc("POT",pot)
1831 call getenv_loc("DIRTMP",tmpdir)
1832 call getenv_loc("CURDIR",curdir)
1833 call getenv_loc("OUT1FILE",out1file_text)
1834 c print *,"Processor",myrank,"fg_rank",fg_rank," did GETENV"
1835 out1file_text=ucase(out1file_text)
1836 if (out1file_text(1:1).eq."Y") then
1839 out1file=fg_rank.gt.0
1844 if (lentmp.gt.0) then
1845 write (*,'(80(1h!))')
1846 write (*,'(a,19x,a,19x,a)') "!"," A T T E N T I O N ","!"
1847 write (*,'(80(1h!))')
1848 write (*,*)"All output files will be on node /tmp directory."
1850 call MPI_GET_PROCESSOR_NAME( nodename, nodelen, IERROR )
1851 if (me.eq.king) then
1852 write (*,*) "The master node is ",nodename
1853 else if (fg_rank.eq.0) then
1854 write (*,*) "I am the CG slave node ",nodename
1856 write (*,*) "I am the FG slave node ",nodename
1859 PREFIX = tmpdir(:lentmp)//'/'//prefix(:lenpre)
1860 lenpre = lentmp+lenpre+1
1862 entname=prefix(:lenpre)//'_'//pot(:lenpot)//'.entr'
1863 C Get the names and open the input files
1864 #if defined(WINIFL) || defined(WINPGI)
1865 open(1,file=pref_orig(:ilen(pref_orig))//
1866 & '.inp',status='old',readonly,shared)
1867 open (9,file=prefix(:ilen(prefix))//'.intin',status='unknown')
1868 C open (18,file=prefix(:ilen(prefix))//'.entin',status='unknown')
1869 C Get parameter filenames and open the parameter files.
1870 call getenv_loc('BONDPAR',bondname)
1871 open (ibond,file=bondname,status='old',readonly,shared)
1872 call getenv_loc('THETPAR',thetname)
1873 open (ithep,file=thetname,status='old',readonly,shared)
1874 call getenv_loc('ROTPAR',rotname)
1875 open (irotam,file=rotname,status='old',readonly,shared)
1876 call getenv_loc('TORPAR',torname)
1877 open (itorp,file=torname,status='old',readonly,shared)
1878 call getenv_loc('TORDPAR',tordname)
1879 open (itordp,file=tordname,status='old',readonly,shared)
1880 call getenv_loc('FOURIER',fouriername)
1881 open (ifourier,file=fouriername,status='old',readonly,shared)
1882 call getenv_loc('ELEPAR',elename)
1883 open (ielep,file=elename,status='old',readonly,shared)
1884 call getenv_loc('SIDEPAR',sidename)
1885 open (isidep,file=sidename,status='old',readonly,shared)
1886 #elif (defined CRAY) || (defined AIX)
1887 open(1,file=pref_orig(:ilen(pref_orig))//'.inp',status='old',
1889 c print *,"Processor",myrank," opened file 1"
1890 open (9,file=prefix(:ilen(prefix))//'.intin',status='unknown')
1891 c print *,"Processor",myrank," opened file 9"
1892 C open (18,file=prefix(:ilen(prefix))//'.entin',status='unknown')
1893 C Get parameter filenames and open the parameter files.
1894 call getenv_loc('BONDPAR',bondname)
1895 open (ibond,file=bondname,status='old',action='read')
1896 c print *,"Processor",myrank," opened file IBOND"
1897 call getenv_loc('THETPAR',thetname)
1898 open (ithep,file=thetname,status='old',action='read')
1899 c print *,"Processor",myrank," opened file ITHEP"
1900 call getenv_loc('ROTPAR',rotname)
1901 open (irotam,file=rotname,status='old',action='read')
1902 c print *,"Processor",myrank," opened file IROTAM"
1903 call getenv_loc('TORPAR',torname)
1904 open (itorp,file=torname,status='old',action='read')
1905 c print *,"Processor",myrank," opened file ITORP"
1906 call getenv_loc('TORDPAR',tordname)
1907 open (itordp,file=tordname,status='old',action='read')
1908 c print *,"Processor",myrank," opened file ITORDP"
1909 call getenv_loc('SCCORPAR',sccorname)
1910 open (isccor,file=sccorname,status='old',action='read')
1911 c print *,"Processor",myrank," opened file ISCCOR"
1912 call getenv_loc('FOURIER',fouriername)
1913 open (ifourier,file=fouriername,status='old',action='read')
1914 c print *,"Processor",myrank," opened file IFOURIER"
1915 call getenv_loc('ELEPAR',elename)
1916 open (ielep,file=elename,status='old',action='read')
1917 c print *,"Processor",myrank," opened file IELEP"
1918 call getenv_loc('SIDEPAR',sidename)
1919 open (isidep,file=sidename,status='old',action='read')
1920 c print *,"Processor",myrank," opened file ISIDEP"
1921 c print *,"Processor",myrank," opened parameter files"
1923 open(1,file=pref_orig(:ilen(pref_orig))//'.inp',status='old')
1924 open (9,file=prefix(:ilen(prefix))//'.intin',status='unknown')
1925 C open (18,file=prefix(:ilen(prefix))//'.entin',status='unknown')
1926 C Get parameter filenames and open the parameter files.
1927 call getenv_loc('BONDPAR',bondname)
1928 open (ibond,file=bondname,status='old')
1929 call getenv_loc('THETPAR',thetname)
1930 open (ithep,file=thetname,status='old')
1931 call getenv_loc('ROTPAR',rotname)
1932 open (irotam,file=rotname,status='old')
1933 call getenv_loc('TORPAR',torname)
1934 open (itorp,file=torname,status='old')
1935 call getenv_loc('TORDPAR',tordname)
1936 open (itordp,file=tordname,status='old')
1937 call getenv_loc('SCCORPAR',sccorname)
1938 open (isccor,file=sccorname,status='old')
1939 call getenv_loc('FOURIER',fouriername)
1940 open (ifourier,file=fouriername,status='old')
1941 call getenv_loc('ELEPAR',elename)
1942 open (ielep,file=elename,status='old')
1943 call getenv_loc('SIDEPAR',sidename)
1944 open (isidep,file=sidename,status='old')
1946 open(1,file=pref_orig(:ilen(pref_orig))//'.inp',status='old',
1948 open (9,file=prefix(:ilen(prefix))//'.intin',status='unknown')
1949 C open (18,file=prefix(:ilen(prefix))//'.entin',status='unknown')
1950 C Get parameter filenames and open the parameter files.
1951 call getenv_loc('BONDPAR',bondname)
1952 open (ibond,file=bondname,status='old',readonly)
1953 call getenv_loc('THETPAR',thetname)
1954 open (ithep,file=thetname,status='old',readonly)
1955 call getenv_loc('ROTPAR',rotname)
1956 open (irotam,file=rotname,status='old',readonly)
1957 call getenv_loc('TORPAR',torname)
1958 open (itorp,file=torname,status='old',readonly)
1959 call getenv_loc('TORDPAR',tordname)
1960 open (itordp,file=tordname,status='old',readonly)
1961 call getenv_loc('SCCORPAR',sccorname)
1962 open (isccor,file=sccorname,status='old',readonly)
1964 call getenv_loc('THETPARPDB',thetname_pdb)
1965 print *,"thetname_pdb ",thetname_pdb
1966 open (ithep_pdb,file=thetname_pdb,status='old',action='read')
1967 print *,ithep_pdb," opened"
1969 call getenv_loc('FOURIER',fouriername)
1970 open (ifourier,file=fouriername,status='old',readonly)
1971 call getenv_loc('ELEPAR',elename)
1972 open (ielep,file=elename,status='old',readonly)
1973 call getenv_loc('SIDEPAR',sidename)
1974 open (isidep,file=sidename,status='old',readonly)
1976 call getenv_loc('ROTPARPDB',rotname_pdb)
1977 open (irotam_pdb,file=rotname_pdb,status='old',action='read')
1982 C 8/9/01 In the newest version SCp interaction constants are read from a file
1983 C Use -DOLDSCP to use hard-coded constants instead.
1985 call getenv_loc('SCPPAR',scpname)
1986 #if defined(WINIFL) || defined(WINPGI)
1987 open (iscpp,file=scpname,status='old',readonly,shared)
1988 #elif (defined CRAY) || (defined AIX)
1989 open (iscpp,file=scpname,status='old',action='read')
1991 open (iscpp,file=scpname,status='old')
1993 open (iscpp,file=scpname,status='old',readonly)
1996 call getenv_loc('PATTERN',patname)
1997 #if defined(WINIFL) || defined(WINPGI)
1998 open (icbase,file=patname,status='old',readonly,shared)
1999 #elif (defined CRAY) || (defined AIX)
2000 open (icbase,file=patname,status='old',action='read')
2002 open (icbase,file=patname,status='old')
2004 open (icbase,file=patname,status='old',readonly)
2007 C Open output file only for CG processes
2008 c print *,"Processor",myrank," fg_rank",fg_rank
2009 if (fg_rank.eq.0) then
2011 if (nodes.eq.1) then
2014 npos = dlog10(dfloat(nodes-1))+1
2016 if (npos.lt.3) npos=3
2017 write (liczba,'(i1)') npos
2018 form = '(bz,i'//liczba(:ilen(liczba))//'.'//liczba(:ilen(liczba))
2020 write (liczba,form) me
2021 outname=prefix(:lenpre)//'.out_'//pot(:lenpot)//
2022 & liczba(:ilen(liczba))
2023 intname=prefix(:lenpre)//'_'//pot(:lenpot)//liczba(:ilen(liczba))
2025 pdbname=prefix(:lenpre)//'_'//pot(:lenpot)//liczba(:ilen(liczba))
2027 mol2name=prefix(:lenpre)//'_'//pot(:lenpot)//
2028 & liczba(:ilen(liczba))//'.mol2'
2029 statname=prefix(:lenpre)//'_'//pot(:lenpot)//
2030 & liczba(:ilen(liczba))//'.stat'
2032 & call copy_to_tmp(pref_orig(:ilen(pref_orig))//'_'//pot(:lenpot)
2033 & //liczba(:ilen(liczba))//'.stat')
2034 rest2name=prefix(:ilen(prefix))//"_"//liczba(:ilen(liczba))
2037 qname=prefix(:lenpre)//'_'//pot(:lenpot)//
2038 & liczba(:ilen(liczba))//'.const'
2043 outname=prefix(:lenpre)//'.out_'//pot(:lenpot)
2044 intname=prefix(:lenpre)//'_'//pot(:lenpot)//'.int'
2045 pdbname=prefix(:lenpre)//'_'//pot(:lenpot)//'.pdb'
2046 mol2name=prefix(:lenpre)//'_'//pot(:lenpot)//'.mol2'
2047 statname=prefix(:lenpre)//'_'//pot(:lenpot)//'.stat'
2049 & call copy_to_tmp(pref_orig(:ile(pref_orig))//'_'//pot(:lenpot)//
2051 rest2name=prefix(:ilen(prefix))//'.rst'
2053 qname=prefix(:lenpre)//'_'//pot(:lenpot)//'.const'
2056 #if defined(AIX) || defined(PGI)
2057 if (me.eq.king .or. .not. out1file)
2058 & open(iout,file=outname,status='unknown')
2060 if (fg_rank.gt.0) then
2061 write (liczba,'(i3.3)') myrank/nfgtasks
2062 write (ll,'(bz,i3.3)') fg_rank
2063 open(iout,file="debug"//liczba(:ilen(liczba))//"."//ll,
2068 open(igeom,file=intname,status='unknown',position='append')
2069 open(ipdb,file=pdbname,status='unknown')
2070 open(imol2,file=mol2name,status='unknown')
2071 open(istat,file=statname,status='unknown',position='append')
2073 c1out open(iout,file=outname,status='unknown')
2076 if (me.eq.king .or. .not.out1file)
2077 & open(iout,file=outname,status='unknown')
2079 if (fg_rank.gt.0) then
2080 write (liczba,'(i3.3)') myrank/nfgtasks
2081 write (ll,'(bz,i3.3)') fg_rank
2082 open(iout,file="debug"//liczba(:ilen(liczba))//"."//ll,
2087 open(igeom,file=intname,status='unknown',access='append')
2088 open(ipdb,file=pdbname,status='unknown')
2089 open(imol2,file=mol2name,status='unknown')
2090 open(istat,file=statname,status='unknown',access='append')
2092 c1out open(iout,file=outname,status='unknown')
2095 csa_rbank=prefix(:lenpre)//'.CSA.rbank'
2096 csa_seed=prefix(:lenpre)//'.CSA.seed'
2097 csa_history=prefix(:lenpre)//'.CSA.history'
2098 csa_bank=prefix(:lenpre)//'.CSA.bank'
2099 csa_bank1=prefix(:lenpre)//'.CSA.bank1'
2100 csa_alpha=prefix(:lenpre)//'.CSA.alpha'
2101 csa_alpha1=prefix(:lenpre)//'.CSA.alpha1'
2102 c!bankt csa_bankt=prefix(:lenpre)//'.CSA.bankt'
2103 csa_int=prefix(:lenpre)//'.int'
2104 csa_bank_reminimized=prefix(:lenpre)//'.CSA.bank_reminimized'
2105 csa_native_int=prefix(:lenpre)//'.CSA.native.int'
2106 csa_in=prefix(:lenpre)//'.CSA.in'
2107 c print *,"Processor",myrank,"fg_rank",fg_rank," opened files"
2110 write (iout,'(80(1h-))')
2111 write (iout,'(30x,a)') "FILE ASSIGNMENT"
2112 write (iout,'(80(1h-))')
2113 write (iout,*) "Input file : ",
2114 & pref_orig(:ilen(pref_orig))//'.inp'
2115 write (iout,*) "Output file : ",
2116 & outname(:ilen(outname))
2118 write (iout,*) "Sidechain potential file : ",
2119 & sidename(:ilen(sidename))
2121 write (iout,*) "SCp potential file : ",
2122 & scpname(:ilen(scpname))
2124 write (iout,*) "Electrostatic potential file : ",
2125 & elename(:ilen(elename))
2126 write (iout,*) "Cumulant coefficient file : ",
2127 & fouriername(:ilen(fouriername))
2128 write (iout,*) "Torsional parameter file : ",
2129 & torname(:ilen(torname))
2130 write (iout,*) "Double torsional parameter file : ",
2131 & tordname(:ilen(tordname))
2132 write (iout,*) "SCCOR parameter file : ",
2133 & sccorname(:ilen(sccorname))
2134 write (iout,*) "Bond & inertia constant file : ",
2135 & bondname(:ilen(bondname))
2136 write (iout,*) "Bending parameter file : ",
2137 & thetname(:ilen(thetname))
2138 write (iout,*) "Rotamer parameter file : ",
2139 & rotname(:ilen(rotname))
2140 write (iout,*) "Thetpdb parameter file : ",
2141 & thetname_pdb(:ilen(thetname_pdb))
2142 write (iout,*) "Threading database : ",
2143 & patname(:ilen(patname))
2145 &write (iout,*)" DIRTMP : ",
2147 write (iout,'(80(1h-))')
2151 c----------------------------------------------------------------------------
2152 subroutine card_concat(card)
2153 implicit real*8 (a-h,o-z)
2154 include 'DIMENSIONS'
2155 include 'COMMON.IOUNITS'
2157 character*80 karta,ucase
2159 read (inp,'(a)') karta
2162 do while (karta(80:80).eq.'&')
2163 card=card(:ilen(card)+1)//karta(:79)
2164 read (inp,'(a)') karta
2167 card=card(:ilen(card)+1)//karta
2170 c----------------------------------------------------------------------------------
2172 implicit real*8 (a-h,o-z)
2173 include 'DIMENSIONS'
2174 include 'COMMON.CHAIN'
2175 include 'COMMON.IOUNITS'
2177 open(irest2,file=rest2name,status='unknown')
2178 read(irest2,*) totT,EK,potE,totE,t_bath
2180 read(irest2,'(3e15.5)') (d_t(j,i),j=1,3)
2183 read(irest2,'(3e15.5)') (dc(j,i),j=1,3)
2186 read (irest2,*) iset
2191 c---------------------------------------------------------------------------------
2192 subroutine read_fragments
2193 implicit real*8 (a-h,o-z)
2194 include 'DIMENSIONS'
2198 include 'COMMON.SETUP'
2199 include 'COMMON.CHAIN'
2200 include 'COMMON.IOUNITS'
2202 include 'COMMON.CONTROL'
2203 read(inp,*) nset,nfrag,npair,nfrag_back
2204 if(me.eq.king.or..not.out1file)
2205 & write(iout,*) "nset",nset," nfrag",nfrag," npair",npair,
2206 & " nfrag_back",nfrag_back
2208 read(inp,*) mset(iset)
2210 read(inp,*) wfrag(i,iset),ifrag(1,i,iset),ifrag(2,i,iset),
2212 if(me.eq.king.or..not.out1file)
2213 & write(iout,*) "R ",i,wfrag(i,iset),ifrag(1,i,iset),
2214 & ifrag(2,i,iset), qinfrag(i,iset)
2217 read(inp,*) wpair(i,iset),ipair(1,i,iset),ipair(2,i,iset),
2219 if(me.eq.king.or..not.out1file)
2220 & write(iout,*) "R ",i,wpair(i,iset),ipair(1,i,iset),
2221 & ipair(2,i,iset), qinpair(i,iset)
2224 read(inp,*) wfrag_back(1,i,iset),wfrag_back(2,i,iset),
2225 & wfrag_back(3,i,iset),
2226 & ifrag_back(1,i,iset),ifrag_back(2,i,iset)
2227 if(me.eq.king.or..not.out1file)
2228 & write(iout,*) "A",i,wfrag_back(1,i,iset),wfrag_back(2,i,iset),
2229 & wfrag_back(3,i,iset),ifrag_back(1,i,iset),ifrag_back(2,i,iset)
2234 c-------------------------------------------------------------------------------
2235 subroutine read_dist_constr
2236 implicit real*8 (a-h,o-z)
2237 include 'DIMENSIONS'
2241 include 'COMMON.SETUP'
2242 include 'COMMON.CONTROL'
2243 include 'COMMON.CHAIN'
2244 include 'COMMON.IOUNITS'
2245 include 'COMMON.SBRIDGE'
2246 integer ifrag_(2,100),ipair_(2,100)
2247 double precision wfrag_(100),wpair_(100)
2248 character*500 controlcard
2249 c write (iout,*) "Calling read_dist_constr"
2250 c write (iout,*) "nres",nres," nstart_sup",nstart_sup," nsup",nsup
2252 call card_concat(controlcard)
2253 call readi(controlcard,"NFRAG",nfrag_,0)
2254 call readi(controlcard,"NPAIR",npair_,0)
2255 call readi(controlcard,"NDIST",ndist_,0)
2256 call reada(controlcard,'DIST_CUT',dist_cut,5.0d0)
2257 call multreadi(controlcard,"IFRAG",ifrag_(1,1),2*nfrag_,0)
2258 call multreadi(controlcard,"IPAIR",ipair_(1,1),2*npair_,0)
2259 call multreada(controlcard,"WFRAG",wfrag_(1),nfrag_,0.0d0)
2260 call multreada(controlcard,"WPAIR",wpair_(1),npair_,0.0d0)
2261 c write (iout,*) "NFRAG",nfrag_," NPAIR",npair_," NDIST",ndist_
2262 c write (iout,*) "IFRAG"
2264 c write (iout,*) i,ifrag_(1,i),ifrag_(2,i),wfrag_(i)
2266 c write (iout,*) "IPAIR"
2268 c write (iout,*) i,ipair_(1,i),ipair_(2,i),wpair_(i)
2272 if (ifrag_(1,i).lt.nstart_sup) ifrag_(1,i)=nstart_sup
2273 if (ifrag_(2,i).gt.nstart_sup+nsup-1)
2274 & ifrag_(2,i)=nstart_sup+nsup-1
2275 c write (iout,*) i,ifrag_(1,i),ifrag_(2,i),wfrag_(i)
2277 if (wfrag_(i).gt.0.0d0) then
2278 do j=ifrag_(1,i),ifrag_(2,i)-1
2279 do k=j+1,ifrag_(2,i)
2280 c write (iout,*) "j",j," k",k
2282 if (constr_dist.eq.1) then
2287 forcon(nhpb)=wfrag_(i)
2288 else if (constr_dist.eq.2) then
2289 if (ddjk.le.dist_cut) then
2294 forcon(nhpb)=wfrag_(i)
2301 forcon(nhpb)=wfrag_(i)*dexp(-0.5d0*(ddjk/dist_cut)**2)
2304 if (.not.out1file .or. me.eq.king)
2305 & write (iout,'(a,3i5,f8.2,1pe12.2)') "+dist.constr ",
2306 & nhpb,ihpb(nhpb),jhpb(nhpb),dhpb(nhpb),forcon(nhpb)
2308 write (iout,'(a,3i5,f8.2,1pe12.2)') "+dist.constr ",
2309 & nhpb,ihpb(nhpb),jhpb(nhpb),dhpb(nhpb),forcon(nhpb)
2316 if (wpair_(i).gt.0.0d0) then
2324 do j=ifrag_(1,ii),ifrag_(2,ii)
2325 do k=ifrag_(1,jj),ifrag_(2,jj)
2329 forcon(nhpb)=wpair_(i)
2330 dhpb(nhpb)=dist(j,k)
2332 if (.not.out1file .or. me.eq.king)
2333 & write (iout,'(a,3i5,f8.2,f10.1)') "+dist.constr ",
2334 & nhpb,ihpb(nhpb),jhpb(nhpb),dhpb(nhpb),forcon(nhpb)
2336 write (iout,'(a,3i5,f8.2,f10.1)') "+dist.constr ",
2337 & nhpb,ihpb(nhpb),jhpb(nhpb),dhpb(nhpb),forcon(nhpb)
2344 read (inp,*) ihpb(nhpb+1),jhpb(nhpb+1),forcon(nhpb+1)
2345 if (forcon(nhpb+1).gt.0.0d0) then
2347 dhpb(nhpb)=dist(ihpb(nhpb),jhpb(nhpb))
2349 if (.not.out1file .or. me.eq.king)
2350 & write (iout,'(a,3i5,f8.2,f10.1)') "+dist.constr ",
2351 & nhpb,ihpb(nhpb),jhpb(nhpb),dhpb(nhpb),forcon(nhpb)
2353 write (iout,'(a,3i5,f8.2,f10.1)') "+dist.constr ",
2354 & nhpb,ihpb(nhpb),jhpb(nhpb),dhpb(nhpb),forcon(nhpb)
2361 c-------------------------------------------------------------------------------
2363 subroutine flush(iu)
2368 subroutine flush(iu)
2373 c------------------------------------------------------------------------------
2374 subroutine copy_to_tmp(source)
2375 include "DIMENSIONS"
2376 include "COMMON.IOUNITS"
2377 character*(*) source
2378 character* 256 tmpfile
2382 tmpfile=curdir(:ilen(curdir))//"/"//source(:ilen(source))
2383 inquire(file=tmpfile,exist=ex)
2385 write (*,*) "Copying ",tmpfile(:ilen(tmpfile)),
2386 & " to temporary directory..."
2387 write (*,*) "/bin/cp "//tmpfile(:ilen(tmpfile))//" "//tmpdir
2388 call system("/bin/cp "//tmpfile(:ilen(tmpfile))//" "//tmpdir)
2392 c------------------------------------------------------------------------------
2393 subroutine move_from_tmp(source)
2394 include "DIMENSIONS"
2395 include "COMMON.IOUNITS"
2396 character*(*) source
2399 write (*,*) "Moving ",source(:ilen(source)),
2400 & " from temporary directory to working directory"
2401 write (*,*) "/bin/mv "//source(:ilen(source))//" "//curdir
2402 call system("/bin/mv "//source(:ilen(source))//" "//curdir)
2405 c------------------------------------------------------------------------------
2406 subroutine random_init(seed)
2408 C Initialize random number generator
2410 implicit real*8 (a-h,o-z)
2411 include 'DIMENSIONS'
2414 logical OKRandom, prng_restart
2416 integer iseed_array(4)
2418 include 'COMMON.IOUNITS'
2419 include 'COMMON.TIME1'
2420 include 'COMMON.THREAD'
2421 include 'COMMON.SBRIDGE'
2422 include 'COMMON.CONTROL'
2423 include 'COMMON.MCM'
2424 include 'COMMON.MAP'
2425 include 'COMMON.HEADER'
2426 include 'COMMON.CSA'
2427 include 'COMMON.CHAIN'
2428 include 'COMMON.MUCA'
2430 include 'COMMON.FFIELD'
2431 include 'COMMON.SETUP'
2432 iseed=-dint(dabs(seed))
2433 if (iseed.eq.0) then
2434 write (iout,'(/80(1h*)/20x,a/80(1h*))')
2435 & 'Random seed undefined. The program will stop.'
2436 write (*,'(/80(1h*)/20x,a/80(1h*))')
2437 & 'Random seed undefined. The program will stop.'
2439 call mpi_finalize(mpi_comm_world,ierr)
2441 stop 'Bad random seed.'
2444 if (fg_rank.eq.0) then
2448 & write (iout,*) 'MPI: node= ', me, ' iseed= ',iseed
2449 OKRandom = prng_restart(me,iseed)
2452 tmp=65536.0d0**(4-i)
2453 iseed_array(i) = dint(seed/tmp)
2454 seed=seed-iseed_array(i)*tmp
2457 & write (iout,*) 'MPI: node= ', me, ' iseed(4)= ',
2458 & (iseed_array(i),i=1,4)
2459 write (*,*) 'MPI: node= ',me, ' iseed(4)= ',
2460 & (iseed_array(i),i=1,4)
2461 OKRandom = prng_restart(me,iseed_array)
2464 c r1 = prng_next(me)
2465 r1=ran_number(0.0D0,1.0D0)
2467 & write (iout,*) 'ran_num',r1
2468 if (r1.lt.0.0d0) OKRandom=.false.
2470 if (.not.OKRandom) then
2471 write (iout,*) 'PRNG IS NOT WORKING!!!'
2472 print *,'PRNG IS NOT WORKING!!!'
2475 call mpi_abort(mpi_comm_world,error_msg,ierr)
2478 write (iout,*) 'too many processors for parallel prng'
2479 write (*,*) 'too many processors for parallel prng'
2487 write (iout,*) 'ran_num',ran_number(0.0d0,1.0d0)