2 !-----------------------------------------------------------------------
8 !-----------------------------------------------------------------------------
11 !-----------------------------------------------------------------------------
13 !-----------------------------------------------------------------------------
15 !-----------------------------------------------------------------------------
16 subroutine write_csa_pdb(var,ene,nft,ik,iw_pdb)
19 use geometry_data, only:nres,nvar
20 use geometry, only:var_to_geom,chainbuild
21 use compare, only:secondary2
22 ! implicit real*8 (a-h,o-z)
23 ! include 'DIMENSIONS'
24 ! include 'COMMON.CSA'
25 ! include 'COMMON.BANK'
26 ! include 'COMMON.VAR'
27 ! include 'COMMON.IOUNITS'
28 ! include 'COMMON.MINIM'
29 ! include 'COMMON.SETUP'
30 ! include 'COMMON.GEO'
31 ! include 'COMMON.CHAIN'
32 ! include 'COMMON.LOCAL'
33 ! include 'COMMON.INTERACT'
34 ! include 'COMMON.NAMES'
35 ! include 'COMMON.SBRIDGE'
36 integer :: lenpre,lenpot !,ilen
38 real(kind=8),dimension(nvar) :: var !(maxvar) (maxvar=6*maxres)
39 character(len=50) :: titelloc
40 character(len=3) :: zahl
41 real(kind=8),dimension(mxch*(mxch+1)/2+1) :: ene
43 integer :: nft,ik,iw_pdb
46 if(ene(1).lt.eglob_csa) then
49 call numstr(nglob_csa,zahl)
51 call var_to_geom(nvar,var)
53 call secondary2(.false.)
56 open(icsa_pdb,file=prefix(:lenpre)//'@'//zahl//'.pdb')
59 write(titelloc,'(a2,i3,a3,i9,a3,i6)') &
60 'GM',nglob_csa,' e ',nft,' m ',nmin_csa
62 write(titelloc,'(a2,i3,a3,i9,a3,i6,a5,f5.2,a5,f5.1)') &
63 'GM',nglob_csa,' e ',nft,' m ',nmin_csa,' rms ',&
64 rmsn(ik),' %NC ',pncn(ik)*100
66 call pdbout(eglob_csa,titelloc,icsa_pdb)
71 end subroutine write_csa_pdb
72 !-----------------------------------------------------------------------------
74 !-----------------------------------------------------------------------------
75 subroutine from_pdb(n,idum)
76 ! This subroutine stores the UNRES int variables generated from
77 ! subroutine readpdb into the 1st conformation of in dihang_in.
78 ! Subsequent n-1 conformations of dihang_in have identical values
79 ! of theta and phi as the 1st conformation but random values for
81 ! The array cref (also generated from subroutine readpdb) is stored
82 ! to crefjlee to be used for rmsd calculation in CSA, if necessary.
86 use random, only: ran1
87 ! implicit real*8 (a-h,o-z)
88 ! include 'DIMENSIONS'
89 ! include 'COMMON.IOUNITS'
90 ! include 'COMMON.CHAIN'
91 ! include 'COMMON.VAR'
92 ! include 'COMMON.BANK'
93 ! include 'COMMON.GEO'
95 integer :: n,idum,m,i,j,k,kk,kkk
100 dihang_in(1,j,1,m)=theta(j+1)
101 dihang_in(2,j,1,m)=phi(j+2)
102 dihang_in(3,j,1,m)=alph(j)
103 dihang_in(4,j,1,m)=omeg(j)
105 dihang_in(2,nres-1,1,k)=0.0d0
109 dihang_in(1,k,1,m)=dihang_in(1,k,1,1)
110 dihang_in(2,k,1,m)=dihang_in(2,k,1,1)
111 if(dabs(dihang_in(3,k,1,1)).gt.1.d-6) then
112 dihang_in(3,k,1,m)=90.d0*ran1(idum)+90.d0
113 dihang_in(3,k,1,m)=dihang_in(3,k,1,m)*deg2rad
115 if(dabs(dihang_in(4,k,1,1)).gt.1.d-6) then
116 dihang_in(4,k,1,m)=360.d0*ran1(idum)-180.d0
117 dihang_in(4,k,1,m)=dihang_in(4,k,1,m)*deg2rad
122 ! Store cref to crefjlee (they are in COMMON.CHAIN).
126 crefjlee(kk,k)=cref(kk,k,kkk)
130 open(icsa_native_int,file=csa_native_int,status="old")
132 write(icsa_native_int,*) m,e
133 write(icsa_native_int,200) &
134 (dihang_in(1,k,1,m)*rad2deg,k=2,nres-1)
135 write(icsa_native_int,200) &
136 (dihang_in(2,k,1,m)*rad2deg,k=2,nres-2)
137 write(icsa_native_int,200) &
138 (dihang_in(3,k,1,m)*rad2deg,k=2,nres-1)
139 write(icsa_native_int,200) &
140 (dihang_in(4,k,1,m)*rad2deg,k=2,nres-1)
144 write(icsa_native_int,200) (crefjlee(i,k),i=1,3)
146 close(icsa_native_int)
151 end subroutine from_pdb
152 !-----------------------------------------------------------------------------
153 subroutine from_int(n,mm,idum)
158 use geometry, only:chainbuild,gen_side
159 use energy, only:etotal
161 ! implicit real*8 (a-h,o-z)
162 ! include 'DIMENSIONS'
163 ! include 'COMMON.IOUNITS'
164 ! include 'COMMON.CHAIN'
165 ! include 'COMMON.VAR'
166 ! include 'COMMON.INTERACT'
167 ! include 'COMMON.BANK'
168 ! include 'COMMON.GEO'
169 ! include 'COMMON.CONTACTS'
173 real(kind=8),dimension(0:n_ene) :: energia
175 integer :: n,mm,idum,i,ii,j,m,k,kk,maxcount_fail,icount_fail,maxsi
178 open(icsa_native_int,file=csa_native_int,status="old")
179 read (icsa_native_int,*)
180 call read_angles(icsa_native_int,*10)
182 10 write (iout,'(2a)') "CHUJ NASTAPIL - error in ",&
183 csa_native_int(:ilen(csa_native_int))
187 dihang_in(1,j,1,1)=theta(j+1)
188 dihang_in(2,j,1,1)=phi(j+2)
189 dihang_in(3,j,1,1)=alph(j)
190 dihang_in(4,j,1,1)=omeg(j)
192 dihang_in(2,nres-1,1,1)=0.0d0
194 ! read(icsa_native_int,*) ind,e
195 ! read(icsa_native_int,200) (dihang_in(1,k,1,1),k=2,nres-1)
196 ! read(icsa_native_int,200) (dihang_in(2,k,1,1),k=2,nres-2)
197 ! read(icsa_native_int,200) (dihang_in(3,k,1,1),k=2,nres-1)
198 ! read(icsa_native_int,200) (dihang_in(4,k,1,1),k=2,nres-1)
199 ! dihang_in(2,nres-1,1,1)=0.d0
206 ! dihang_in(1,k,1,m)=dihang_in(1,k,1,1)
207 ! dihang_in(2,k,1,m)=dihang_in(2,k,1,1)
208 ! if(abs(dihang_in(3,k,1,1)).gt.1.d-3) then
209 ! dihang_in(3,k,1,m)=90.d0*ran1(idum)+90.d0
211 ! if(abs(dihang_in(4,k,1,1)).gt.1.d-3) then
212 ! dihang_in(4,k,1,m)=360.d0*ran1(idum)-180.d0
220 DO WHILE (FAIL .AND. ICOUNT_FAIL .LE. MAXCOUNT_FAIL)
223 if (itype(i,1).ne.10) then
224 !d print *,'i=',i,' itype=',itype(i,1),' theta=',theta(i+1)
227 do while (fail .and. ii .le. maxsi)
228 call gen_side(itype(i,1),theta(i+1),alph(i),omeg(i),fail,molnum(i))
235 fail = (energia(0).ge.1.0d20)
236 icount_fail=icount_fail+1
240 if (icount_fail.gt.maxcount_fail) then
242 'Failed to generate non-overlaping near-native conf.',&
247 dihang_in(1,j,1,m)=theta(j+1)
248 dihang_in(2,j,1,m)=phi(j+2)
249 dihang_in(3,j,1,m)=alph(j)
250 dihang_in(4,j,1,m)=omeg(j)
252 dihang_in(2,nres-1,1,m)=0.0d0
256 ! write(icsa_native_int,*) m,e
257 ! write(icsa_native_int,200) (dihang_in(1,k,1,m),k=2,nres-1)
258 ! write(icsa_native_int,200) (dihang_in(2,k,1,m),k=2,nres-2)
259 ! write(icsa_native_int,200) (dihang_in(3,k,1,m),k=2,nres-1)
260 ! write(icsa_native_int,200) (dihang_in(4,k,1,m),k=2,nres-1)
262 ! close(icsa_native_int)
267 ! dihang_in(i,j,1,m)=dihang_in(i,j,1,m)*deg2rad
272 call dihang_to_c(dihang_in(1,1,1,1))
274 ! Store c to cref (they are in COMMON.CHAIN).
277 crefjlee(kk,k)=c(kk,k)
281 call contact(.true.,ncont_ref,icont_ref,co)
284 ! write(icsa_native_int,200) (crefjlee(i,k),i=1,3)
286 close(icsa_native_int)
291 end subroutine from_int
292 !-----------------------------------------------------------------------------
293 subroutine dihang_to_c(aarray)
297 use geometry, only:chainbuild
298 ! implicit real*8 (a-h,o-z)
299 ! include 'DIMENSIONS'
300 ! include 'COMMON.CSA'
301 ! include 'COMMON.BANK'
302 ! include 'COMMON.CHAIN'
303 ! include 'COMMON.GEO'
304 ! include 'COMMON.VAR'
306 real(kind=8),dimension(mxang,nres,mxch) :: aarray !(mxang,maxres,mxch)
309 ! phi(i)=dihang_in(1,i-2,1,1)
312 theta(i+1)=aarray(1,i,1)
313 phi(i+2)=aarray(2,i,1)
314 alph(i)=aarray(3,i,1)
315 omeg(i)=aarray(4,i,1)
321 end subroutine dihang_to_c
322 !-----------------------------------------------------------------------------
324 !-----------------------------------------------------------------------------
326 subroutine cartout(time)
328 subroutine cartoutx(time)
330 use geometry_data, only: c,nres
332 use MD_data, only: potE,t_bath
333 ! implicit real*8 (a-h,o-z)
334 ! include 'DIMENSIONS'
335 ! include 'COMMON.CHAIN'
336 ! include 'COMMON.INTERACT'
337 ! include 'COMMON.NAMES'
338 ! include 'COMMON.IOUNITS'
339 ! include 'COMMON.HEADER'
340 ! include 'COMMON.SBRIDGE'
341 ! include 'COMMON.DISTFIT'
342 ! include 'COMMON.MD'
347 #if defined(AIX) || defined(PGI)
348 open(icart,file=cartname,position="append")
350 open(icart,file=cartname,access="append")
352 write (icart,'(e15.8,2e15.5,f12.5,$)') time,potE,uconst,t_bath
354 write (icart,'(i4,$)') &
355 nss,(idssb(j)+nres,jdssb(j)+nres,j=1,nss)
357 write (icart,'(i4,$)') &
358 nss,(ihpb(j),jhpb(j),j=1,nss)
360 write (icart,'(i4,20f7.4)') nfrag+npair+3*nfrag_back,&
361 (qfrag(i),i=1,nfrag),(qpair(i),i=1,npair),&
362 (utheta(i),ugamma(i),uscdiff(i),i=1,nfrag_back)
363 write (icart,'(8f10.5)') &
364 ((c(k,j),k=1,3),j=1,nres),&
365 ((c(k,j+nres),k=1,3),j=nnt,nct)
370 end subroutine cartout
372 end subroutine cartoutx
374 !-----------------------------------------------------------------------------
376 subroutine cartout(time)
377 ! implicit real*8 (a-h,o-z)
378 ! include 'DIMENSIONS'
379 use geometry_data, only: c,nres
381 use MD_data, only: potE,t_bath
385 ! include 'COMMON.SETUP'
387 integer,parameter :: me=0
389 ! include 'COMMON.CHAIN'
390 ! include 'COMMON.INTERACT'
391 ! include 'COMMON.NAMES'
392 ! include 'COMMON.IOUNITS'
393 ! include 'COMMON.HEADER'
394 ! include 'COMMON.SBRIDGE'
395 ! include 'COMMON.DISTFIT'
396 ! include 'COMMON.MD'
400 real(kind=4),dimension(3,2*nres+2) :: xcoord !(3,maxres2+2) (maxres2=2*maxres
405 call xdrfopen_(ixdrf,cartname, "a", iret)
406 call xdrffloat_(ixdrf, real(time), iret)
407 call xdrffloat_(ixdrf, real(potE), iret)
408 call xdrffloat_(ixdrf, real(uconst), iret)
409 call xdrffloat_(ixdrf, real(uconst_back), iret)
410 call xdrffloat_(ixdrf, real(t_bath), iret)
411 call xdrfint_(ixdrf, nss, iret)
414 call xdrfint_(ixdrf, idssb(j)+nres, iret)
415 call xdrfint_(ixdrf, jdssb(j)+nres, iret)
417 call xdrfint_(ixdrf, ihpb(j), iret)
418 call xdrfint_(ixdrf, jhpb(j), iret)
421 call xdrfint_(ixdrf, nfrag+npair+3*nfrag_back, iret)
423 call xdrffloat_(ixdrf, real(qfrag(i)), iret)
426 call xdrffloat_(ixdrf, real(qpair(i)), iret)
429 call xdrffloat_(ixdrf, real(utheta(i)), iret)
430 call xdrffloat_(ixdrf, real(ugamma(i)), iret)
431 call xdrffloat_(ixdrf, real(uscdiff(i)), iret)
434 call xdrfopen(ixdrf,cartname, "a", iret)
435 call xdrffloat(ixdrf, real(time), iret)
436 call xdrffloat(ixdrf, real(potE), iret)
437 call xdrffloat(ixdrf, real(uconst), iret)
438 call xdrffloat(ixdrf, real(uconst_back), iret)
439 call xdrffloat(ixdrf, real(t_bath), iret)
440 call xdrfint(ixdrf, nss, iret)
443 call xdrfint(ixdrf, idssb(j)+nres, iret)
444 call xdrfint(ixdrf, jdssb(j)+nres, iret)
446 call xdrfint(ixdrf, ihpb(j), iret)
447 call xdrfint(ixdrf, jhpb(j), iret)
450 call xdrfint(ixdrf, nfrag+npair+3*nfrag_back, iret)
452 call xdrffloat(ixdrf, real(qfrag(i)), iret)
455 call xdrffloat(ixdrf, real(qpair(i)), iret)
458 call xdrffloat(ixdrf, real(utheta(i)), iret)
459 call xdrffloat(ixdrf, real(ugamma(i)), iret)
460 call xdrffloat(ixdrf, real(uscdiff(i)), iret)
471 xcoord(j,nres+i-nnt+1)=c(j,i+nres)
477 call xdrf3dfcoord_(ixdrf, xcoord, itmp, prec, iret)
478 call xdrfclose_(ixdrf, iret)
480 call xdrf3dfcoord(ixdrf, xcoord, itmp, prec, iret)
481 call xdrfclose(ixdrf, iret)
484 end subroutine cartout
486 !-----------------------------------------------------------------------------
487 subroutine statout(itime)
493 use compare, only:rms_nac_nnc
494 ! implicit real*8 (a-h,o-z)
495 ! include 'DIMENSIONS'
496 ! include 'COMMON.CONTROL'
497 ! include 'COMMON.CHAIN'
498 ! include 'COMMON.INTERACT'
499 ! include 'COMMON.NAMES'
500 ! include 'COMMON.IOUNITS'
501 ! include 'COMMON.HEADER'
502 ! include 'COMMON.SBRIDGE'
503 ! include 'COMMON.DISTFIT'
504 ! include 'COMMON.MD'
505 ! include 'COMMON.REMD'
506 ! include 'COMMON.SETUP'
508 real(kind=8),dimension(0:n_ene) :: energia
509 ! double precision gyrate
511 !el common /gucio/ cm
512 character(len=256) :: line1,line2
513 character(len=4) :: format1,format2
514 character(len=30) :: format
516 integer :: i,ii1,ii2,j
517 real(kind=8) :: rms,frac,frac_nn,co,distance
521 open(istat,file=statname,position="append")
525 open(istat,file=statname,position="append")
527 open(istat,file=statname,access="append")
530 if (AFMlog.gt.0) then
532 call rms_nac_nnc(rms,frac,frac_nn,co,.false.)
533 write (line1,'(i10,f15.2,3f12.3,f7.2,2f6.3,4f12.3,i5,$)')&
534 itime,totT,EK,potE,totE,&
535 rms,frac,frac_nn,kinetic_T,t_bath,gyrate(),&
539 !C print *,'A CHUJ',potEcomp(23)
540 write (line1,'(i10,f15.2,7f12.3,i5,$)') &
541 itime,totT,EK,potE,totE,&
542 kinetic_T,t_bath,gyrate(),&
546 else if (selfguide.gt.0) then
549 distance=distance+(c(j,afmend)-c(j,afmbeg))**2
551 distance=dsqrt(distance)
553 call rms_nac_nnc(rms,frac,frac_nn,co,.false.)
554 write (line1,'(i10,f15.2,3f12.3,f7.2,2f6.3,f12.3,f10.1,2f8.2, &
556 itime,totT,EK,potE,totE,&
557 rms,frac,frac_nn,kinetic_T,t_bath,gyrate(),&
558 distance,potEcomp(23),me
562 !C print *,'A CHUJ',potEcomp(23)
563 write (line1,'(i10,f15.2,8f12.3,i5,$)')&
564 itime,totT,EK,potE,totE, &
565 kinetic_T,t_bath,gyrate(),&
566 distance,potEcomp(23),me
571 call rms_nac_nnc(rms,frac,frac_nn,co,.false.)
572 write (line1,'(i10,f15.2,3f12.3,f7.2,4f6.3,3f12.3,i5,$)') &
573 itime,totT,EK,potE,totE,&
574 rms,frac,frac_nn,co,amax,kinetic_T,t_bath,gyrate(),me
577 write (line1,'(i10,f15.2,7f12.3,i5,$)') &
578 itime,totT,EK,potE,totE,&
579 amax,kinetic_T,t_bath,gyrate(),me
583 if(usampl.and.totT.gt.eq_time) then
584 write(line2,'(i5,2f9.4,300f7.4)') iset,uconst,uconst_back,&
585 (qfrag(ii1),ii1=1,nfrag),(qpair(ii2),ii2=1,npair),&
586 (utheta(i),ugamma(i),uscdiff(i),i=1,nfrag_back)
587 write(format2,'(a1,i3.3)') "a",23+7*nfrag+7*npair &
593 if (print_compon) then
595 write(format,'(a1,a4,a1,a4,a10)') "(",format1,",",format2,&
597 write (istat,format) "#","",&
598 (ename(print_order(i)),i=1,nprint_ene)
600 write(format,'(a1,a4,a1,a4,a10)') "(",format1,",",format2,&
602 write (istat,format) line1,line2,&
603 (potEcomp(print_order(i)),i=1,nprint_ene)
605 write(format,'(a1,a4,a1,a4,a1)') "(",format1,",",format2,")"
606 write (istat,format) line1,line2
614 end subroutine statout
615 !-----------------------------------------------------------------------------
617 !-----------------------------------------------------------------------------
623 use muca_md, only:read_muca
624 ! implicit real*8 (a-h,o-z)
625 ! include 'DIMENSIONS'
629 ! include 'COMMON.SETUP'
630 ! include 'COMMON.CONTROL'
631 ! include 'COMMON.SBRIDGE'
632 ! include 'COMMON.IOUNITS'
633 logical :: file_exist
635 ! Read force-field parameters except weights
637 ! Read job setup parameters
639 ! Read force-field parameters except weights
642 ! Read control parameters for energy minimzation if required
643 if (minim) call read_minim
644 ! Read MCM control parameters if required
645 if (modecalc.eq.3 .or. modecalc.eq.6) call mcmread
646 ! Read MD control parameters if reqjuired
647 if (modecalc.eq.12) call read_MDpar
648 ! Read MREMD control parameters if required
649 if (modecalc.eq.14) then
653 ! Read MUCA control parameters if required
654 if (lmuca) call read_muca
655 ! Read CSA control parameters if required (from fort.40 if exists
656 ! otherwise from general input file)
657 if (modecalc.eq.8) then
658 inquire (file="fort.40",exist=file_exist)
659 if (.not.file_exist) call csaread
661 !fmc if (modecalc.eq.10) call mcmfread
662 ! Read molecule information, molecule geometry, energy-term weights, and
663 ! restraints if requested
665 ! Print restraint information
667 if (.not. out1file .or. me.eq.king) then
670 write (iout,'(a,i5,a)') "The following",nhpb-nss,&
671 " distance constraints have been imposed"
673 write (iout,'(3i6,f10.5)') i-nss,ihpb(i),jhpb(i),forcon(i)
678 ! print *,"Processor",myrank," leaves READRTNS"
679 ! write(iout,*) "end readrtns"
681 end subroutine readrtns
682 !-----------------------------------------------------------------------------
685 ! Read molecular data.
687 ! use control, only: ilen
693 use MD_data, only: t_bath
695 use compare, only:seq_comp,contact
697 ! implicit real*8 (a-h,o-z)
698 ! include 'DIMENSIONS'
701 integer :: error_msg,ierror,ierr,ierrcode
703 ! include 'COMMON.IOUNITS'
704 ! include 'COMMON.GEO'
705 ! include 'COMMON.VAR'
706 ! include 'COMMON.INTERACT'
707 ! include 'COMMON.LOCAL'
708 ! include 'COMMON.NAMES'
709 ! include 'COMMON.CHAIN'
710 ! include 'COMMON.FFIELD'
711 ! include 'COMMON.SBRIDGE'
712 ! include 'COMMON.HEADER'
713 ! include 'COMMON.CONTROL'
714 ! include 'COMMON.DBASE'
715 ! include 'COMMON.THREAD'
716 ! include 'COMMON.CONTACTS'
717 ! include 'COMMON.TORCNSTR'
718 ! include 'COMMON.TIME1'
719 ! include 'COMMON.BOUNDS'
720 ! include 'COMMON.MD'
721 ! include 'COMMON.SETUP'
722 character(len=4),dimension(:,:),allocatable :: sequence !(maxres,maxmolecules)
724 ! double precision x(maxvar)
725 character(len=256) :: pdbfile
726 character(len=800) :: weightcard
727 character(len=80) :: weightcard_t!,ucase
728 ! integer,dimension(:),allocatable :: itype_pdb !(maxres)
729 ! common /pizda/ itype_pdb
730 logical :: fail !seq_comp,
731 real(kind=8) :: energia(0:n_ene)
735 integer :: i,j,l,k,kkk,ii,i1,i2,it1,it2,mnum
737 real(kind=8),dimension(3,maxres2+2) :: c_alloc
738 real(kind=8),dimension(3,0:maxres2) :: dc_alloc
739 real(kind=8),dimension(:,:), allocatable :: secprob
740 integer,dimension(maxres) :: itype_alloc
742 integer :: iti,nsi,maxsi,itrial,itmp
743 real(kind=8) :: wlong,scalscp,co,ssscale,phihel,phibet,sigmahel,&
745 allocate(weights(n_ene))
746 !-----------------------------
747 allocate(c(3,2*maxres+2)) !(3,maxres2+2) maxres2=2*maxres
748 allocate(dc(3,0:2*maxres)) !(3,0:maxres2)
749 allocate(itype(maxres,5)) !(maxres)
750 allocate(istype(maxres))
757 !-----------------------------
761 ! Read weights of the subsequent energy terms.
762 call card_concat(weightcard,.true.)
763 call reada(weightcard,'WLONG',wlong,1.0D0)
764 call reada(weightcard,'WSC',wsc,wlong)
765 call reada(weightcard,'WSCP',wscp,wlong)
766 call reada(weightcard,'WELEC',welec,1.0D0)
767 call reada(weightcard,'WVDWPP',wvdwpp,welec)
768 call reada(weightcard,'WEL_LOC',wel_loc,1.0D0)
769 call reada(weightcard,'WCORR4',wcorr4,0.0D0)
770 call reada(weightcard,'WCORR5',wcorr5,0.0D0)
771 call reada(weightcard,'WCORR6',wcorr6,0.0D0)
772 call reada(weightcard,'WTURN3',wturn3,1.0D0)
773 call reada(weightcard,'WTURN4',wturn4,1.0D0)
774 call reada(weightcard,'WTURN6',wturn6,1.0D0)
775 call reada(weightcard,'WSCCOR',wsccor,1.0D0)
776 call reada(weightcard,'WSTRAIN',wstrain,1.0D0)
777 call reada(weightcard,'WVDWPP_NUCL',wvdwpp_nucl,0.0D0)
778 call reada(weightcard,'WELPP',welpp,0.0d0)
779 call reada(weightcard,'WVDWPSB',wvdwpsb,0.0d0)
780 call reada(weightcard,'WELPSB',welpsb,0.0D0)
781 call reada(weightcard,'WVDWSB',wvdwsb,0.0d0)
782 call reada(weightcard,'WELSB',welsb,0.0D0)
783 call reada(weightcard,'WBOND_NUCL',wbond_nucl,0.0D0)
784 call reada(weightcard,'WANG_NUCL',wang_nucl,0.0D0)
785 call reada(weightcard,'WSBLOC',wsbloc,0.0D0)
786 call reada(weightcard,'WTOR_NUCL',wtor_nucl,0.0D0)
787 ! print *,"KUR..",wtor_nucl
788 call reada(weightcard,'WTORD_NUCL',wtor_d_nucl,0.0D0)
789 call reada(weightcard,'WCORR_NUCL',wcorr_nucl,0.0D0)
790 call reada(weightcard,'WCORR3_NUC',wcorr3_nucl,0.0D0)
791 call reada(weightcard,'WBOND',wbond,1.0D0)
792 call reada(weightcard,'WTOR',wtor,1.0D0)
793 call reada(weightcard,'WTORD',wtor_d,1.0D0)
794 call reada(weightcard,'WSHIELD',wshield,0.05D0)
795 call reada(weightcard,'LIPSCALE',lipscale,1.0D0)
796 call reada(weightcard,'WLT',wliptran,1.0D0)
797 call reada(weightcard,'WTUBE',wtube,1.0d0)
798 call reada(weightcard,'WANG',wang,1.0D0)
799 call reada(weightcard,'WSCLOC',wscloc,1.0D0)
800 call reada(weightcard,'SCAL14',scal14,0.4D0)
801 call reada(weightcard,'SCALSCP',scalscp,1.0d0)
802 call reada(weightcard,'CUTOFF',cutoff_corr,7.0d0)
803 call reada(weightcard,'DELT_CORR',delt_corr,0.5d0)
804 call reada(weightcard,'TEMP0',temp0,300.0d0)
805 call reada(weightcard,'WSCBASE',wscbase,0.0D0)
806 if (index(weightcard,'SOFT').gt.0) ipot=6
807 call reada(weightcard,'WBOND_NUCL',wbond_nucl,0.0D0)
808 call reada(weightcard,'WCATCAT',wcatcat,0.0d0)
809 call reada(weightcard,'WCATPROT',wcatprot,0.0d0)
810 call reada(weightcard,'WCATNUCL',wcatnucl,0.0d0)
811 call reada(weightcard,'WCATTRAN',wcat_tran,0.0d0)
812 call reada(weightcard,'WPEPBASE',wpepbase,1.0d0)
813 call reada(weightcard,'WSCPHO',wscpho,0.0d0)
814 call reada(weightcard,'WPEPPHO',wpeppho,0.0d0)
816 ! 12/1/95 Added weight for the multi-body term WCORR
817 call reada(weightcard,'WCORRH',wcorr,1.0D0)
818 if (wcorr4.gt.0.0d0) wcorr=wcorr4
838 weights(26)=wvdwpp_nucl
844 weights(32)=wbond_nucl
845 weights(33)=wang_nucl
847 weights(35)=wtor_nucl
848 weights(36)=wtor_d_nucl
849 weights(37)=wcorr_nucl
850 weights(38)=wcorr3_nucl
858 weights(56)=wcat_tran
859 if(me.eq.king.or..not.out1file) &
860 write (iout,10) wsc,wscp,welec,wvdwpp,wbond,wang,wscloc,wtor,&
861 wtor_d,wstrain,wel_loc,wcorr,wcorr5,wcorr6,wsccor,wturn3,&
863 10 format (/'Energy-term weights (unscaled):'// &
864 'WSCC= ',f10.6,' (SC-SC)'/ &
865 'WSCP= ',f10.6,' (SC-p)'/ &
866 'WELEC= ',f10.6,' (p-p electr)'/ &
867 'WVDWPP= ',f10.6,' (p-p VDW)'/ &
868 'WBOND= ',f10.6,' (stretching)'/ &
869 'WANG= ',f10.6,' (bending)'/ &
870 'WSCLOC= ',f10.6,' (SC local)'/ &
871 'WTOR= ',f10.6,' (torsional)'/ &
872 'WTORD= ',f10.6,' (double torsional)'/ &
873 'WSTRAIN=',f10.6,' (SS bridges & dist. cnstr.)'/ &
874 'WEL_LOC=',f10.6,' (multi-body 3-rd order)'/ &
875 'WCORR4= ',f10.6,' (multi-body 4th order)'/ &
876 'WCORR5= ',f10.6,' (multi-body 5th order)'/ &
877 'WCORR6= ',f10.6,' (multi-body 6th order)'/ &
878 'WSCCOR= ',f10.6,' (back-scloc correlation)'/ &
879 'WTURN3= ',f10.6,' (turns, 3rd order)'/ &
880 'WTURN4= ',f10.6,' (turns, 4th order)'/ &
881 'WTURN6= ',f10.6,' (turns, 6th order)')
882 if(me.eq.king.or..not.out1file)then
883 if (wcorr4.gt.0.0d0) then
884 write (iout,'(/2a/)') 'Local-electrostatic type correlation ',&
885 'between contact pairs of peptide groups'
886 write (iout,'(2(a,f5.3/))') &
887 'Cutoff on 4-6th order correlation terms: ',cutoff_corr,&
888 'Range of quenching the correlation terms:',2*delt_corr
889 else if (wcorr.gt.0.0d0) then
890 write (iout,'(/2a/)') 'Hydrogen-bonding correlation ',&
891 'between contact pairs of peptide groups'
893 write (iout,'(a,f8.3)') &
894 'Scaling factor of 1,4 SC-p interactions:',scal14
895 write (iout,'(a,f8.3)') &
896 'General scaling factor of SC-p interactions:',scalscp
898 r0_corr=cutoff_corr-delt_corr
900 aad(i,1)=scalscp*aad(i,1)
901 aad(i,2)=scalscp*aad(i,2)
902 bad(i,1)=scalscp*bad(i,1)
903 bad(i,2)=scalscp*bad(i,2)
905 call rescale_weights(t_bath)
906 if(me.eq.king.or..not.out1file) &
907 write (iout,22) wsc,wscp,welec,wvdwpp,wbond,wang,wscloc,wtor,&
908 wtor_d,wstrain,wel_loc,wcorr,wcorr5,wcorr6,wsccor,wturn3,&
910 22 format (/'Energy-term weights (scaled):'// &
911 'WSCC= ',f10.6,' (SC-SC)'/ &
912 'WSCP= ',f10.6,' (SC-p)'/ &
913 'WELEC= ',f10.6,' (p-p electr)'/ &
914 'WVDWPP= ',f10.6,' (p-p VDW)'/ &
915 'WBOND= ',f10.6,' (stretching)'/ &
916 'WANG= ',f10.6,' (bending)'/ &
917 'WSCLOC= ',f10.6,' (SC local)'/ &
918 'WTOR= ',f10.6,' (torsional)'/ &
919 'WTORD= ',f10.6,' (double torsional)'/ &
920 'WSTRAIN=',f10.6,' (SS bridges & dist. cnstr.)'/ &
921 'WEL_LOC=',f10.6,' (multi-body 3-rd order)'/ &
922 'WCORR4= ',f10.6,' (multi-body 4th order)'/ &
923 'WCORR5= ',f10.6,' (multi-body 5th order)'/ &
924 'WCORR6= ',f10.6,' (multi-body 6th order)'/ &
925 'WSCCOR= ',f10.6,' (back-scloc correlatkion)'/ &
926 'WTURN3= ',f10.6,' (turns, 3rd order)'/ &
927 'WTURN4= ',f10.6,' (turns, 4th order)'/ &
928 'WTURN6= ',f10.6,' (turns, 6th order)')
929 if(me.eq.king.or..not.out1file) &
930 write (iout,*) "Reference temperature for weights calculation:",&
932 call reada(weightcard,"D0CM",d0cm,3.78d0)
933 call reada(weightcard,"AKCM",akcm,15.1d0)
934 call reada(weightcard,"AKTH",akth,11.0d0)
935 call reada(weightcard,"AKCT",akct,12.0d0)
936 call reada(weightcard,"V1SS",v1ss,-1.08d0)
937 call reada(weightcard,"V2SS",v2ss,7.61d0)
938 call reada(weightcard,"V3SS",v3ss,13.7d0)
939 call reada(weightcard,"EBR",ebr,-5.50D0)
940 call reada(weightcard,"ATRISS",atriss,0.301D0)
941 call reada(weightcard,"BTRISS",btriss,0.021D0)
942 call reada(weightcard,"CTRISS",ctriss,1.001D0)
943 call reada(weightcard,"DTRISS",dtriss,1.001D0)
944 call reada(weightcard,"SSSCALE",ssscale,1.0D0)
945 dyn_ss=(index(weightcard,'DYN_SS').gt.0)
947 call reada(weightcard,"HT",Ht,0.0D0)
949 ss_depth=(ebr/wsc-0.25*eps(1,1))*ssscale
950 Ht=(Ht/wsc-0.25*eps(1,1))*ssscale
951 akcm=akcm/wsc*ssscale
952 akth=akth/wsc*ssscale
953 akct=akct/wsc*ssscale
954 v1ss=v1ss/wsc*ssscale
955 v2ss=v2ss/wsc*ssscale
956 v3ss=v3ss/wsc*ssscale
958 ss_depth=ebr/wstrain-0.25*eps(1,1)*wsc/wstrain
961 if(me.eq.king.or..not.out1file) then
962 write (iout,*) "Parameters of the SS-bond potential:"
963 write (iout,*) "D0CM",d0cm," AKCM",akcm," AKTH",akth,&
965 write (iout,*) "V1SS",v1ss," V2SS",v2ss," V3SS",v3ss
966 write (iout,*) "EBR",ebr," SS_DEPTH",ss_depth
967 write (iout,*)" HT",Ht
968 print *,'indpdb=',indpdb,' pdbref=',pdbref
970 if (indpdb.gt.0 .or. pdbref) then
971 read(inp,'(a)') pdbfile
972 if(me.eq.king.or..not.out1file) &
973 write (iout,'(2a)') 'PDB data will be read from file ',&
974 pdbfile(:ilen(pdbfile))
975 open(ipdbin,file=pdbfile,status='old',err=33)
977 33 write (iout,'(a)') 'Error opening PDB file.'
980 ! print *,'Begin reading pdb data'
982 ! call int_from_cart1(.true.)
984 ! print *,'Finished reading pdb data'
985 if(me.eq.king.or..not.out1file) &
986 write (iout,'(a,i3,a,i3)')'nsup=',nsup,&
987 ' nstart_sup=',nstart_sup !,"ergwergewrgae"
988 !el if(.not.allocated(itype_pdb))
989 allocate(itype_pdb(nres))
991 itype_pdb(i)=itype(i,1)
995 nct=nstart_sup+nsup-1
996 !el if(.not.allocated(icont_ref))
997 allocate(icont_ref(2,(nres/2)*nres)) ! maxcont=12*maxres
998 call contact(.false.,ncont_ref,icont_ref,co)
1001 if(me.eq.king.or..not.out1file) &
1002 write(iout,*)'Adding sidechains'
1006 if (iti.ne.10 .and. itype(i,1).ne.ntyp1) then
1009 do while (fail.and.nsi.le.maxsi)
1010 call gen_side(iti,theta(i+1),alph(i),omeg(i),fail,molnum(i))
1013 if(fail) write(iout,*)'Adding sidechain failed for res ',&
1014 i,' after ',nsi,' trials'
1019 print *,"CZY TU DOCHODZE"
1020 if (indpdb.eq.0) then
1022 allocate(sequence(maxres,5))
1026 ! Read sequence if not taken from the pdb file.
1028 read (inp,*) nres_molec(molec)
1029 print *,'nres=',nres
1030 if (iscode.gt.0) then
1031 read (inp,'(80a1)') (sequence(i,molec)(1:1),i=1,nres_molec(molec))
1033 read (inp,'(20(1x,a3))') (sequence(i,molec),i=1,nres_molec(molec))
1035 ! read(inp,*) weightcard_t
1036 ! print *,"po seq" weightcard_t
1037 ! Convert sequence to numeric code
1039 do i=1,nres_molec(molec)
1041 itype(i,1)=rescode(i,sequence(i,molec),iscode,molec)
1046 ! read(inp,*) weightcard_t
1047 ! print *,"po seq", weightcard_t
1050 ! Read sequence if not taken from the pdb file.
1052 read (inp,*) nres_molec(molec)
1053 print *,'nres=',nres_molec(molec)
1054 ! allocate(sequence(maxres,5))
1055 ! if (iscode.gt.0) then
1056 read (inp,'(20a4)') (sequence(i,molec),i=1,nres_molec(molec))
1058 print *,(sequence(i,molec),i=1,nres_molec(molec))
1059 ! Convert sequence to numeric code
1061 do i=1,nres_molec(molec)
1063 istype(itmp)=sugarcode(sequence(i,molec)(1:1),i)
1064 sequence(i,molec)=sequence(i,molec)(1:2)
1065 itype(itmp,molec)=rescode(i,sequence(i,molec),iscode,molec)
1066 write(iout,*) "NUCLE=", itype(itmp,molec)
1071 ! Read sequence if not taken from the pdb file.
1073 read (inp,*) nres_molec(molec)
1074 ! print *,'nres=',nres
1075 read (inp,'(20(1x,a3))') (sequence(i,molec),i=1,nres_molec(molec))
1076 ! Convert sequence to numeric code
1077 print *,nres_molec(molec)
1078 do i=1,nres_molec(molec)
1081 itype(itmp,molec)=rescode(i,sequence(i,molec),iscode,molec)
1086 nres=nres+nres_molec(i)
1087 print *,"nres_molec",nres,nres_molec(i)
1090 ! Assign initial virtual bond lengths
1091 if(.not.allocated(molnum)) then
1092 allocate(molnum(nres+1))
1095 do j=1,nres_molec(i)
1100 ! print *,nres_molec(i)
1103 if(.not.allocated(vbld)) then
1104 print *, "I DO ENTER"
1105 allocate(vbld(2*nres))
1107 if(.not.allocated(vbld_inv)) allocate(vbld_inv(2*nres))
1110 if (molnum(i).eq.1) then
1115 write(iout,*) "typy",itype(i,mnum),ntyp1_molec(mnum),i
1118 if ((itype(i,mnum).eq.ntyp1_molec(mnum)).or.&
1119 (itype(i-1,mnum).eq.ntyp1_molec(mnum))) then
1126 if (molnum(i).eq.1) then
1127 ! print *, "molnum",molnum(i),itype(i,molnum(i)),nres,i
1128 vbld(i+nres)=dsc(iabs(itype(i,molnum(i))))
1129 vbld_inv(i+nres)=dsc_inv(iabs(itype(i,molnum(i))))
1131 vbld(i+nres)=vbldsc0_nucl(1,iabs(itype(i,molnum(i))))
1132 vbld_inv(i+nres)=1.0/vbldsc0_nucl(1,iabs(itype(i,molnum(i))))
1134 ! write (iout,*) "i",i," itype",itype(i,1),
1135 ! & " dsc",dsc(itype(i,1))," vbld",vbld(i),vbld(i+nres)
1139 ! print '(20i4)',(itype(i,1),i=1,nres)
1140 !----------------------------
1141 !el reallocate tables
1144 ! c_alloc(j,i)=c(j,i)
1145 ! dc_alloc(j,i)=dc(j,i)
1149 !elwrite(iout,*) "itype",i,itype(i,1)
1150 ! itype_alloc(i)=itype(i,1)
1156 ! allocate(c(3,2*nres+4))
1157 ! allocate(dc(3,0:2*nres+2))
1158 ! allocate(itype(nres+2))
1159 allocate(itel(nres+2))
1164 ! c(j,i)=c_alloc(j,i)
1165 ! dc(j,i)=dc_alloc(j,i)
1169 ! itype(i,1)=itype_alloc(i)
1172 !--------------------------
1175 if (itype(i,1).eq.ntyp1 .or. itype(i+1,1).eq.ntyp1) then
1177 if (itype(i,1).eq.ntyp1) then
1181 else if (iabs(itype(i+1,1)).ne.20) then
1183 else if (iabs(itype(i,1)).ne.20) then
1190 if(me.eq.king.or..not.out1file)then
1191 write (iout,*) "ITEL"
1194 write (iout,*) i,itype(i,1),itel(i)
1196 print *,'Call Read_Bridge.'
1199 !--------------------------------
1200 ! print *,"tu dochodze"
1201 ! znamy nres oraz nss można zaalokowac potrzebne tablice
1202 call alloc_geo_arrays
1203 call alloc_ener_arrays
1204 !--------------------------------
1205 ! 8/13/98 Set limits to generating the dihedral angles
1210 read (inp,*) ndih_constr
1211 if (ndih_constr.gt.0) then
1213 allocate(idih_constr(ndih_constr),idih_nconstr(ndih_constr)) !(maxdih_constr)
1214 allocate(phi0(ndih_constr),drange(ndih_constr)) !(maxdih_constr)
1215 allocate(ftors(ndih_constr)) !(maxdih_constr)
1217 ! read (inp,*) ftors
1218 read (inp,*) (idih_constr(i),phi0(i),drange(i),ftors(i), &
1220 if(me.eq.king.or..not.out1file)then
1222 'There are',ndih_constr,' constraints on phi angles.'
1224 write (iout,'(i5,3f8.3)') idih_constr(i),phi0(i),drange(i), &
1229 phi0(i)=deg2rad*phi0(i)
1230 drange(i)=deg2rad*drange(i)
1232 ! if(me.eq.king.or..not.out1file) &
1233 ! write (iout,*) 'FTORS',ftors
1236 phibound(1,ii) = phi0(i)-drange(i)
1237 phibound(2,ii) = phi0(i)+drange(i)
1239 else if (ndih_constr.lt.0) then
1241 allocate(idih_constr(nres))
1242 allocate(secprob(3,nres))
1243 allocate(vpsipred(3,nres))
1244 allocate(sdihed(2,nres))
1245 call card_concat(weightcard,.true.)
1246 call reada(weightcard,"PHIHEL",phihel,50.0D0)
1247 call reada(weightcard,"PHIBET",phibet,180.0D0)
1248 call reada(weightcard,"SIGMAHEL",sigmahel,30.0d0)
1249 call reada(weightcard,"SIGMABET",sigmabet,40.0d0)
1250 call reada(weightcard,"WDIHC",wdihc,0.591D0)
1251 write (iout,*) "Weight of dihedral angle restraints",wdihc
1252 read(inp,'(9x,3f7.3)') &
1253 (secprob(1,i),secprob(2,i),secprob(3,i),i=nnt,nct)
1254 write (iout,*) "The secprob array"
1256 write (iout,'(i5,3f8.3)') i,(secprob(j,i),j=1,3)
1260 if (itype(i-3,1).ne.ntyp1 .and. itype(i-2,1).ne.ntyp1 &
1261 .and. itype(i-1,1).ne.ntyp1 .and. itype(i,1).ne.ntyp1) then
1262 ndih_constr=ndih_constr+1
1263 idih_constr(ndih_constr)=i
1266 vpsipred(j,ndih_constr)=secprob(j,i-1)*secprob(j,i-2)
1267 sumv=sumv+vpsipred(j,ndih_constr)
1270 vpsipred(j,ndih_constr)=vpsipred(j,ndih_constr)/sumv
1272 phibound(1,ndih_constr)=phihel*deg2rad
1273 phibound(2,ndih_constr)=phibet*deg2rad
1274 sdihed(1,ndih_constr)=sigmahel*deg2rad
1275 sdihed(2,ndih_constr)=sigmabet*deg2rad
1280 if (with_theta_constr) then
1281 !C with_theta_constr is keyword allowing for occurance of theta constrains
1282 read (inp,*) ntheta_constr
1283 !C ntheta_constr is the number of theta constrains
1284 if (ntheta_constr.gt.0) then
1285 !C read (inp,*) ftors
1286 allocate(itheta_constr(ntheta_constr))
1287 allocate(theta_constr0(ntheta_constr))
1288 allocate(theta_drange(ntheta_constr),for_thet_constr(ntheta_constr))
1289 read (inp,*) (itheta_constr(i),theta_constr0(i), &
1290 theta_drange(i),for_thet_constr(i), &
1292 !C the above code reads from 1 to ntheta_constr
1293 !C itheta_constr(i) residue i for which is theta_constr
1294 !C theta_constr0 the global minimum value
1295 !C theta_drange is range for which there is no energy penalty
1296 !C for_thet_constr is the force constant for quartic energy penalty
1298 if(me.eq.king.or..not.out1file)then
1300 'There are',ntheta_constr,' constraints on phi angles.'
1301 do i=1,ntheta_constr
1302 write (iout,'(i5,3f8.3)') itheta_constr(i),theta_constr0(i), &
1307 do i=1,ntheta_constr
1308 theta_constr0(i)=deg2rad*theta_constr0(i)
1309 theta_drange(i)=deg2rad*theta_drange(i)
1311 !C if(me.eq.king.or..not.out1file)
1312 !C & write (iout,*) 'FTORS',ftors
1313 !C do i=1,ntheta_constr
1314 !C ii = itheta_constr(i)
1315 !C thetabound(1,ii) = phi0(i)-drange(i)
1316 !C thetabound(2,ii) = phi0(i)+drange(i)
1318 endif ! ntheta_constr.gt.0
1319 endif! with_theta_constr
1323 if (me.eq.king) then
1325 write (iout,'(a)') 'Boundaries in phi angle sampling:'
1327 write (iout,'(a3,i5,2f10.1)') &
1328 restyp(itype(i,1),1),i,phibound(1,i)*rad2deg,phibound(2,i)*rad2deg
1334 print *,'NNT=',NNT,' NCT=',NCT
1335 if (itype(1,molnum(1)).eq.ntyp1_molec(molnum(1))) nnt=2
1336 if (itype(nres,molnum(nres)).eq.ntyp1_molec(molnum(nres))) nct=nct-1
1338 if(me.eq.king.or..not.out1file) &
1339 write (iout,'(a,i3)') 'nsup=',nsup
1341 if (nsup.le.(nct-nnt+1)) then
1342 do i=0,nct-nnt+1-nsup
1343 if (seq_comp(itype(nnt+i,1),itype_pdb(nstart_sup),nsup)) then
1348 write (iout,'(a)') &
1349 'Error - sequences to be superposed do not match.'
1352 do i=0,nsup-(nct-nnt+1)
1353 if (seq_comp(itype(nnt,1),itype_pdb(nstart_sup+i),nct-nnt+1)) &
1355 nstart_sup=nstart_sup+i
1360 write (iout,'(a)') &
1361 'Error - sequences to be superposed do not match.'
1364 if (nsup.eq.0) nsup=nct-nnt+1
1365 if (nstart_sup.eq.0) nstart_sup=nnt
1366 if (nstart_seq.eq.0) nstart_seq=nnt
1367 if(me.eq.king.or..not.out1file) &
1368 write (iout,*) 'nsup=',nsup,' nstart_sup=',nstart_sup,&
1369 ' nstart_seq=',nstart_seq !,"242343453254"
1371 !--- Zscore rms -------
1372 if (nz_start.eq.0) nz_start=nnt
1373 if (nz_end.eq.0 .and. nsup.gt.0) then
1375 else if (nz_end.eq.0) then
1378 if(me.eq.king.or..not.out1file)then
1379 write (iout,*) 'NZ_START=',nz_start,' NZ_END=',nz_end
1380 write (iout,*) 'IZ_SC=',iz_sc, 'NCT=',nct
1382 !----------------------
1385 if (.not.pdbref) then
1386 call read_angles(inp,*38)
1388 38 write (iout,'(a)') 'Error reading reference structure.'
1390 call MPI_Finalize(MPI_COMM_WORLD,IERROR)
1391 stop 'Error reading reference structure'
1395 !zscore call geom_to_var(nvar,coord_exp_zs(1,1))
1402 cref(j,i,kkk)=c(j,i)
1405 call contact(.true.,ncont_ref,icont_ref,co)
1407 ! write (iout,*) "constr_dist",constr_dist,nstart_sup,nsup
1409 !EL if (constr_dist.gt.0) call read_dist_constr
1410 !EL write (iout,*) "After read_dist_constr nhpb",nhpb
1411 !EL if ((AFMlog.gt.0).or.(selfguide.gt.0)) call read_afminp
1412 !EL call hpb_partition
1413 if(me.eq.king.or..not.out1file) &
1414 write (iout,*) 'Contact order:',co
1416 if(me.eq.king.or..not.out1file) &
1417 write (2,*) 'Shifting contacts:',nstart_seq,nstart_sup
1420 icont_ref(j,i)=icont_ref(j,i)+nstart_seq-nstart_sup
1422 if(me.eq.king.or..not.out1file) &
1423 write (2,*) i,' ',restyp(itype(icont_ref(1,i),1),1),' ',&
1424 icont_ref(1,i),' ',&
1425 restyp(itype(icont_ref(2,i),1),1),' ',icont_ref(2,i)
1429 if (constr_dist.gt.0) call read_dist_constr
1430 write (iout,*) "After read_dist_constr nhpb",nhpb
1431 if ((AFMlog.gt.0).or.(selfguide.gt.0)) call read_afminp
1434 if (indpdb.eq.0 .and. modecalc.ne.2 .and. modecalc.ne.4 &
1435 .and. modecalc.ne.8 .and. modecalc.ne.9 .and. &
1436 modecalc.ne.10) then
1437 ! If input structure hasn't been supplied from the PDB file read or generate
1439 if (iranconf.eq.0 .and. .not. extconf) then
1440 if(me.eq.king.or..not.out1file .and.fg_rank.eq.0) &
1441 write (iout,'(a)') 'Initial geometry will be read in.'
1443 read(inp,'(8f10.5)',end=36,err=36) &
1444 ((c(l,k),l=1,3),k=1,nres),&
1445 ((c(l,k+nres),l=1,3),k=nnt,nct)
1446 write (iout,*) "Exit READ_CART"
1447 write (iout,'(8f10.5)') &
1448 ((c(l,k),l=1,3),k=1,nres)
1449 write (iout,'(8f10.5)') &
1450 ((c(l,k+nres),l=1,3),k=nnt,nct)
1451 call int_from_cart1(.true.)
1452 write (iout,*) "Finish INT_TO_CART"
1455 dc(j,i)=c(j,i+1)-c(j,i)
1456 dc_norm(j,i)=dc_norm(j,i)*vbld_inv(i+1)
1460 if (itype(i,1).ne.10 .and. itype(i,1).ne.ntyp1) then
1462 dc(j,i+nres)=c(j,i+nres)-c(j,i)
1463 dc_norm(j,i+nres)=dc_norm(j,i+nres)*vbld_inv(i+nres)
1469 write(iout,*) "read angles from input"
1470 call read_angles(inp,*36)
1475 36 write (iout,'(a)') 'Error reading angle file.'
1477 call mpi_finalize( MPI_COMM_WORLD,IERR )
1479 stop 'Error reading angle file.'
1481 else if (extconf) then
1482 if(me.eq.king.or..not.out1file .and. fg_rank.eq.0) &
1483 write (iout,'(a)') 'Extended chain initial geometry.'
1485 theta(i)=90d0*deg2rad
1486 if (molnum(i).eq.2) theta(i)=160d0*deg2rad
1489 phi(i)=180d0*deg2rad
1490 if (molnum(i).eq.2) phi(i)=30d0*deg2rad
1493 alph(i)=110d0*deg2rad
1494 if (molnum(i).eq.2) alph(i)=30d0*deg2rad
1497 omeg(i)=-120d0*deg2rad
1498 if (molnum(i).eq.2) omeg(i)=60d0*deg2rad
1499 if (itype(i,1).le.0) omeg(i)=-omeg(i)
1503 if(me.eq.king.or..not.out1file) &
1504 write (iout,'(a)') 'Random-generated initial geometry.'
1508 if (me.eq.king .or. fg_rank.eq.0 .and. &
1509 ( modecalc.eq.12 .or. modecalc.eq.14) ) then
1513 call gen_rand_conf(itmp,*30)
1515 30 write (iout,*) 'Failed to generate random conformation',&
1517 write (*,*) 'Processor:',me,&
1518 ' Failed to generate random conformation',&
1528 write (iout,'(a,i3,a)') 'Processor:',me,&
1529 ' error in generating random conformation.'
1530 write (*,'(a,i3,a)') 'Processor:',me,&
1531 ' error in generating random conformation.'
1534 call MPI_Abort(mpi_comm_world,error_msg,ierrcode)
1540 call gen_rand_conf(itmp,*335)
1542 335 write (iout,*) 'Failed to generate random conformation',&
1544 write (*,*) 'Failed to generate random conformation',&
1547 write (iout,'(a,i3,a)') 'Processor:',me,&
1548 ' error in generating random conformation.'
1549 write (*,'(a,i3,a)') 'Processor:',me,&
1550 ' error in generating random conformation.'
1555 elseif (modecalc.eq.4) then
1556 read (inp,'(a)') intinname
1557 open (intin,file=intinname,status='old',err=333)
1558 if (me.eq.king .or. .not.out1file.and.fg_rank.eq.0) &
1559 write (iout,'(a)') 'intinname',intinname
1560 write (*,'(a)') 'Processor',myrank,' intinname',intinname
1562 333 write (iout,'(2a)') 'Error opening angle file ',intinname
1564 call MPI_Finalize(MPI_COMM_WORLD,IERR)
1566 stop 'Error opening angle file.'
1570 ! Generate distance constraints, if the PDB structure is to be regularized.
1571 if (nthread.gt.0) then
1572 call read_threadbase
1575 if (me.eq.king .or. .not. out1file) &
1577 if (ns.gt.0 .and. (me.eq.king .or. .not.out1file) ) then
1578 write (iout,'(/a,i3,a)') &
1579 'The chain contains',ns,' disulfide-bridging cysteines.'
1580 write (iout,'(20i4)') (iss(i),i=1,ns)
1582 write(iout,*)"Running with dynamic disulfide-bond formation"
1584 write (iout,'(/a/)') 'Pre-formed links are:'
1590 if (me.eq.king.or..not.out1file) &
1591 write (iout,'(2a,i3,3a,i3,a,3f10.3)') &
1592 restyp(it1,1),'(',i1,') -- ',restyp(it2,1),'(',i2,')',dhpb(i),&
1598 if (ns.gt.0.and.dyn_ss) then
1602 forcon(i-nss)=forcon(i)
1609 dyn_ss_mask(iss(i))=.true.
1612 if (i2ndstr.gt.0) call secstrp2dihc
1613 if (indpdb.gt.0) then
1614 write(iout,*) "WCHODZE TU!!"
1615 call int_from_cart1(.true.)
1617 ! call geom_to_var(nvar,x)
1618 ! call etotal(energia(0))
1619 ! call enerprint(energia(0))
1620 ! call briefout(0,etot)
1622 !d write (iout,'(2(a,i3))') 'NNT',NNT,' NCT',NCT
1623 !d write (iout,'(a)') 'Variable list:'
1624 !d write (iout,'(i4,f10.5)') (i,rad2deg*x(i),i=1,nvar)
1626 if (me.eq.king .or. (fg_rank.eq.0 .and. .not.out1file)) &
1627 write (iout,'(//80(1h*)/20x,a,i4,a/80(1h*)//)') &
1628 'Processor',myrank,': end reading molecular data.'
1631 end subroutine molread
1632 !-----------------------------------------------------------------------------
1633 !-----------------------------------------------------------------------------