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)
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 control parameters for energy minimzation if required
640 if (minim) call read_minim
641 ! Read MCM control parameters if required
642 if (modecalc.eq.3 .or. modecalc.eq.6) call mcmread
643 ! Read MD control parameters if reqjuired
644 if (modecalc.eq.12) call read_MDpar
645 ! Read MREMD control parameters if required
646 if (modecalc.eq.14) then
650 ! Read MUCA control parameters if required
651 if (lmuca) call read_muca
652 ! Read CSA control parameters if required (from fort.40 if exists
653 ! otherwise from general input file)
654 if (modecalc.eq.8) then
655 inquire (file="fort.40",exist=file_exist)
656 if (.not.file_exist) call csaread
658 !fmc if (modecalc.eq.10) call mcmfread
659 ! Read molecule information, molecule geometry, energy-term weights, and
660 ! restraints if requested
662 ! Print restraint information
664 if (.not. out1file .or. me.eq.king) then
667 write (iout,'(a,i5,a)') "The following",nhpb-nss,&
668 " distance constraints have been imposed"
670 write (iout,'(3i6,f10.5)') i-nss,ihpb(i),jhpb(i),forcon(i)
675 ! print *,"Processor",myrank," leaves READRTNS"
676 ! write(iout,*) "end readrtns"
678 end subroutine readrtns
679 !-----------------------------------------------------------------------------
682 ! Read molecular data.
684 ! use control, only: ilen
690 use MD_data, only: t_bath
692 use compare, only:seq_comp,contact
694 ! implicit real*8 (a-h,o-z)
695 ! include 'DIMENSIONS'
698 integer :: error_msg,ierror,ierr,ierrcode
700 ! include 'COMMON.IOUNITS'
701 ! include 'COMMON.GEO'
702 ! include 'COMMON.VAR'
703 ! include 'COMMON.INTERACT'
704 ! include 'COMMON.LOCAL'
705 ! include 'COMMON.NAMES'
706 ! include 'COMMON.CHAIN'
707 ! include 'COMMON.FFIELD'
708 ! include 'COMMON.SBRIDGE'
709 ! include 'COMMON.HEADER'
710 ! include 'COMMON.CONTROL'
711 ! include 'COMMON.DBASE'
712 ! include 'COMMON.THREAD'
713 ! include 'COMMON.CONTACTS'
714 ! include 'COMMON.TORCNSTR'
715 ! include 'COMMON.TIME1'
716 ! include 'COMMON.BOUNDS'
717 ! include 'COMMON.MD'
718 ! include 'COMMON.SETUP'
719 character(len=4),dimension(:),allocatable :: sequence !(maxres)
721 ! double precision x(maxvar)
722 character(len=256) :: pdbfile
723 character(len=320) :: weightcard
724 character(len=80) :: weightcard_t!,ucase
725 ! integer,dimension(:),allocatable :: itype_pdb !(maxres)
726 ! common /pizda/ itype_pdb
727 logical :: fail !seq_comp,
728 real(kind=8) :: energia(0:n_ene)
732 integer :: i,j,l,k,kkk,ii,i1,i2,it1,it2
734 real(kind=8),dimension(3,maxres2+2) :: c_alloc
735 real(kind=8),dimension(3,0:maxres2) :: dc_alloc
736 integer,dimension(maxres) :: itype_alloc
738 integer :: iti,nsi,maxsi,itrial,itmp
739 real(kind=8) :: wlong,scalscp,co,ssscale
740 allocate(weights(n_ene))
741 !-----------------------------
742 allocate(c(3,2*maxres+2)) !(3,maxres2+2) maxres2=2*maxres
743 allocate(dc(3,0:2*maxres)) !(3,0:maxres2)
744 allocate(itype(maxres,5)) !(maxres)
751 !-----------------------------
755 ! Read weights of the subsequent energy terms.
756 call card_concat(weightcard,.true.)
757 call reada(weightcard,'WLONG',wlong,1.0D0)
758 call reada(weightcard,'WSC',wsc,wlong)
759 call reada(weightcard,'WSCP',wscp,wlong)
760 call reada(weightcard,'WELEC',welec,1.0D0)
761 call reada(weightcard,'WVDWPP',wvdwpp,welec)
762 call reada(weightcard,'WEL_LOC',wel_loc,1.0D0)
763 call reada(weightcard,'WCORR4',wcorr4,0.0D0)
764 call reada(weightcard,'WCORR5',wcorr5,0.0D0)
765 call reada(weightcard,'WCORR6',wcorr6,0.0D0)
766 call reada(weightcard,'WTURN3',wturn3,1.0D0)
767 call reada(weightcard,'WTURN4',wturn4,1.0D0)
768 call reada(weightcard,'WTURN6',wturn6,1.0D0)
769 call reada(weightcard,'WSCCOR',wsccor,1.0D0)
770 call reada(weightcard,'WSTRAIN',wstrain,1.0D0)
771 call reada(weightcard,'WBOND',wbond,1.0D0)
772 call reada(weightcard,'WTOR',wtor,1.0D0)
773 call reada(weightcard,'WTORD',wtor_d,1.0D0)
774 call reada(weightcard,'WSHIELD',wshield,0.05D0)
775 call reada(weightcard,'LIPSCALE',lipscale,1.0D0)
776 call reada(weightcard,'WLT',wliptran,1.0D0)
777 call reada(weightcard,'WTUBE',wtube,1.0d0)
778 call reada(weightcard,'WANG',wang,1.0D0)
779 call reada(weightcard,'WSCLOC',wscloc,1.0D0)
780 call reada(weightcard,'SCAL14',scal14,0.4D0)
781 call reada(weightcard,'SCALSCP',scalscp,1.0d0)
782 call reada(weightcard,'CUTOFF',cutoff_corr,7.0d0)
783 call reada(weightcard,'DELT_CORR',delt_corr,0.5d0)
784 call reada(weightcard,'TEMP0',temp0,300.0d0)
785 if (index(weightcard,'SOFT').gt.0) ipot=6
786 ! 12/1/95 Added weight for the multi-body term WCORR
787 call reada(weightcard,'WCORRH',wcorr,1.0D0)
788 if (wcorr4.gt.0.0d0) wcorr=wcorr4
808 if(me.eq.king.or..not.out1file) &
809 write (iout,10) wsc,wscp,welec,wvdwpp,wbond,wang,wscloc,wtor,&
810 wtor_d,wstrain,wel_loc,wcorr,wcorr5,wcorr6,wsccor,wturn3,&
812 10 format (/'Energy-term weights (unscaled):'// &
813 'WSCC= ',f10.6,' (SC-SC)'/ &
814 'WSCP= ',f10.6,' (SC-p)'/ &
815 'WELEC= ',f10.6,' (p-p electr)'/ &
816 'WVDWPP= ',f10.6,' (p-p VDW)'/ &
817 'WBOND= ',f10.6,' (stretching)'/ &
818 'WANG= ',f10.6,' (bending)'/ &
819 'WSCLOC= ',f10.6,' (SC local)'/ &
820 'WTOR= ',f10.6,' (torsional)'/ &
821 'WTORD= ',f10.6,' (double torsional)'/ &
822 'WSTRAIN=',f10.6,' (SS bridges & dist. cnstr.)'/ &
823 'WEL_LOC=',f10.6,' (multi-body 3-rd order)'/ &
824 'WCORR4= ',f10.6,' (multi-body 4th order)'/ &
825 'WCORR5= ',f10.6,' (multi-body 5th order)'/ &
826 'WCORR6= ',f10.6,' (multi-body 6th order)'/ &
827 'WSCCOR= ',f10.6,' (back-scloc correlation)'/ &
828 'WTURN3= ',f10.6,' (turns, 3rd order)'/ &
829 'WTURN4= ',f10.6,' (turns, 4th order)'/ &
830 'WTURN6= ',f10.6,' (turns, 6th order)')
831 if(me.eq.king.or..not.out1file)then
832 if (wcorr4.gt.0.0d0) then
833 write (iout,'(/2a/)') 'Local-electrostatic type correlation ',&
834 'between contact pairs of peptide groups'
835 write (iout,'(2(a,f5.3/))') &
836 'Cutoff on 4-6th order correlation terms: ',cutoff_corr,&
837 'Range of quenching the correlation terms:',2*delt_corr
838 else if (wcorr.gt.0.0d0) then
839 write (iout,'(/2a/)') 'Hydrogen-bonding correlation ',&
840 'between contact pairs of peptide groups'
842 write (iout,'(a,f8.3)') &
843 'Scaling factor of 1,4 SC-p interactions:',scal14
844 write (iout,'(a,f8.3)') &
845 'General scaling factor of SC-p interactions:',scalscp
847 r0_corr=cutoff_corr-delt_corr
849 aad(i,1)=scalscp*aad(i,1)
850 aad(i,2)=scalscp*aad(i,2)
851 bad(i,1)=scalscp*bad(i,1)
852 bad(i,2)=scalscp*bad(i,2)
854 call rescale_weights(t_bath)
855 if(me.eq.king.or..not.out1file) &
856 write (iout,22) wsc,wscp,welec,wvdwpp,wbond,wang,wscloc,wtor,&
857 wtor_d,wstrain,wel_loc,wcorr,wcorr5,wcorr6,wsccor,wturn3,&
859 22 format (/'Energy-term weights (scaled):'// &
860 'WSCC= ',f10.6,' (SC-SC)'/ &
861 'WSCP= ',f10.6,' (SC-p)'/ &
862 'WELEC= ',f10.6,' (p-p electr)'/ &
863 'WVDWPP= ',f10.6,' (p-p VDW)'/ &
864 'WBOND= ',f10.6,' (stretching)'/ &
865 'WANG= ',f10.6,' (bending)'/ &
866 'WSCLOC= ',f10.6,' (SC local)'/ &
867 'WTOR= ',f10.6,' (torsional)'/ &
868 'WTORD= ',f10.6,' (double torsional)'/ &
869 'WSTRAIN=',f10.6,' (SS bridges & dist. cnstr.)'/ &
870 'WEL_LOC=',f10.6,' (multi-body 3-rd order)'/ &
871 'WCORR4= ',f10.6,' (multi-body 4th order)'/ &
872 'WCORR5= ',f10.6,' (multi-body 5th order)'/ &
873 'WCORR6= ',f10.6,' (multi-body 6th order)'/ &
874 'WSCCOR= ',f10.6,' (back-scloc correlatkion)'/ &
875 'WTURN3= ',f10.6,' (turns, 3rd order)'/ &
876 'WTURN4= ',f10.6,' (turns, 4th order)'/ &
877 'WTURN6= ',f10.6,' (turns, 6th order)')
878 if(me.eq.king.or..not.out1file) &
879 write (iout,*) "Reference temperature for weights calculation:",&
881 call reada(weightcard,"D0CM",d0cm,3.78d0)
882 call reada(weightcard,"AKCM",akcm,15.1d0)
883 call reada(weightcard,"AKTH",akth,11.0d0)
884 call reada(weightcard,"AKCT",akct,12.0d0)
885 call reada(weightcard,"V1SS",v1ss,-1.08d0)
886 call reada(weightcard,"V2SS",v2ss,7.61d0)
887 call reada(weightcard,"V3SS",v3ss,13.7d0)
888 call reada(weightcard,"EBR",ebr,-5.50D0)
889 call reada(weightcard,"ATRISS",atriss,0.301D0)
890 call reada(weightcard,"BTRISS",btriss,0.021D0)
891 call reada(weightcard,"CTRISS",ctriss,1.001D0)
892 call reada(weightcard,"DTRISS",dtriss,1.001D0)
893 call reada(weightcard,"SSSCALE",ssscale,1.0D0)
894 dyn_ss=(index(weightcard,'DYN_SS').gt.0)
896 call reada(weightcard,"HT",Ht,0.0D0)
898 ss_depth=(ebr/wsc-0.25*eps(1,1))*ssscale
899 Ht=(Ht/wsc-0.25*eps(1,1))*ssscale
900 akcm=akcm/wsc*ssscale
901 akth=akth/wsc*ssscale
902 akct=akct/wsc*ssscale
903 v1ss=v1ss/wsc*ssscale
904 v2ss=v2ss/wsc*ssscale
905 v3ss=v3ss/wsc*ssscale
907 ss_depth=ebr/wstrain-0.25*eps(1,1)*wsc/wstrain
910 if(me.eq.king.or..not.out1file) then
911 write (iout,*) "Parameters of the SS-bond potential:"
912 write (iout,*) "D0CM",d0cm," AKCM",akcm," AKTH",akth,&
914 write (iout,*) "V1SS",v1ss," V2SS",v2ss," V3SS",v3ss
915 write (iout,*) "EBR",ebr," SS_DEPTH",ss_depth
916 write (iout,*)" HT",Ht
917 print *,'indpdb=',indpdb,' pdbref=',pdbref
919 if (indpdb.gt.0 .or. pdbref) then
920 read(inp,'(a)') pdbfile
921 if(me.eq.king.or..not.out1file) &
922 write (iout,'(2a)') 'PDB data will be read from file ',&
923 pdbfile(:ilen(pdbfile))
924 open(ipdbin,file=pdbfile,status='old',err=33)
926 33 write (iout,'(a)') 'Error opening PDB file.'
929 ! print *,'Begin reading pdb data'
931 ! print *,'Finished reading pdb data'
932 if(me.eq.king.or..not.out1file) &
933 write (iout,'(a,i3,a,i3)')'nsup=',nsup,&
934 ' nstart_sup=',nstart_sup !,"ergwergewrgae"
935 !el if(.not.allocated(itype_pdb))
936 allocate(itype_pdb(nres))
938 itype_pdb(i)=itype(i,1)
942 nct=nstart_sup+nsup-1
943 !el if(.not.allocated(icont_ref))
944 allocate(icont_ref(2,12*nres)) ! maxcont=12*maxres
945 call contact(.false.,ncont_ref,icont_ref,co)
948 if(me.eq.king.or..not.out1file) &
949 write(iout,*)'Adding sidechains'
953 if (iti.ne.10 .and. itype(i,1).ne.ntyp1) then
956 do while (fail.and.nsi.le.maxsi)
957 call gen_side(iti,theta(i+1),alph(i),omeg(i),fail)
960 if(fail) write(iout,*)'Adding sidechain failed for res ',&
961 i,' after ',nsi,' trials'
967 if (indpdb.eq.0) then
968 ! Read sequence if not taken from the pdb file.
970 ! print *,'nres=',nres
971 allocate(sequence(nres))
972 if (iscode.gt.0) then
973 read (inp,'(80a1)') (sequence(i)(1:1),i=1,nres)
975 read (inp,'(20(1x,a3))') (sequence(i),i=1,nres)
977 ! Convert sequence to numeric code
979 itype(i,1)=rescode(i,sequence(i),iscode)
981 ! Assign initial virtual bond lengths
982 !elwrite(iout,*) "test_alloc"
983 if(.not.allocated(vbld)) allocate(vbld(2*nres))
984 !elwrite(iout,*) "test_alloc"
985 if(.not.allocated(vbld_inv)) allocate(vbld_inv(2*nres))
986 !elwrite(iout,*) "test_alloc"
992 vbld(i+nres)=dsc(iabs(itype(i,1)))
993 vbld_inv(i+nres)=dsc_inv(iabs(itype(i,1)))
994 ! write (iout,*) "i",i," itype",itype(i,1),
995 ! & " dsc",dsc(itype(i,1))," vbld",vbld(i),vbld(i+nres)
999 ! print '(20i4)',(itype(i,1),i=1,nres)
1000 !----------------------------
1001 !el reallocate tables
1004 ! c_alloc(j,i)=c(j,i)
1005 ! dc_alloc(j,i)=dc(j,i)
1009 !elwrite(iout,*) "itype",i,itype(i,1)
1010 ! itype_alloc(i)=itype(i,1)
1016 ! allocate(c(3,2*nres+4))
1017 ! allocate(dc(3,0:2*nres+2))
1018 ! allocate(itype(nres+2))
1019 allocate(itel(nres+2))
1024 ! c(j,i)=c_alloc(j,i)
1025 ! dc(j,i)=dc_alloc(j,i)
1029 ! itype(i,1)=itype_alloc(i)
1032 !--------------------------
1035 if (itype(i,1).eq.ntyp1 .or. itype(i+1,1).eq.ntyp1) then
1037 if (itype(i,1).eq.ntyp1) then
1041 else if (iabs(itype(i+1,1)).ne.20) then
1043 else if (iabs(itype(i,1)).ne.20) then
1050 if(me.eq.king.or..not.out1file)then
1051 write (iout,*) "ITEL"
1053 write (iout,*) i,itype(i,1),itel(i)
1055 print *,'Call Read_Bridge.'
1058 !--------------------------------
1059 ! znamy nres oraz nss można zaalokowac potrzebne tablice
1060 call alloc_geo_arrays
1061 call alloc_ener_arrays
1062 !--------------------------------
1063 ! 8/13/98 Set limits to generating the dihedral angles
1068 read (inp,*) ndih_constr
1069 if (ndih_constr.gt.0) then
1070 allocate(idih_constr(ndih_constr),idih_nconstr(ndih_constr)) !(maxdih_constr)
1071 allocate(phi0(ndih_constr),drange(ndih_constr)) !(maxdih_constr)
1074 read (inp,*) (idih_constr(i),phi0(i),drange(i),i=1,ndih_constr)
1075 if(me.eq.king.or..not.out1file)then
1077 'There are',ndih_constr,' constraints on phi angles.'
1079 write (iout,'(i5,2f8.3)') idih_constr(i),phi0(i),drange(i)
1083 phi0(i)=deg2rad*phi0(i)
1084 drange(i)=deg2rad*drange(i)
1086 if(me.eq.king.or..not.out1file) &
1087 write (iout,*) 'FTORS',ftors
1090 phibound(1,ii) = phi0(i)-drange(i)
1091 phibound(2,ii) = phi0(i)+drange(i)
1094 if (with_theta_constr) then
1095 !C with_theta_constr is keyword allowing for occurance of theta constrains
1096 read (inp,*) ntheta_constr
1097 !C ntheta_constr is the number of theta constrains
1098 if (ntheta_constr.gt.0) then
1099 !C read (inp,*) ftors
1100 allocate(itheta_constr(ntheta_constr))
1101 allocate(theta_constr0(ntheta_constr))
1102 allocate(theta_drange(ntheta_constr),for_thet_constr(ntheta_constr))
1103 read (inp,*) (itheta_constr(i),theta_constr0(i), &
1104 theta_drange(i),for_thet_constr(i), &
1106 !C the above code reads from 1 to ntheta_constr
1107 !C itheta_constr(i) residue i for which is theta_constr
1108 !C theta_constr0 the global minimum value
1109 !C theta_drange is range for which there is no energy penalty
1110 !C for_thet_constr is the force constant for quartic energy penalty
1112 if(me.eq.king.or..not.out1file)then
1114 'There are',ntheta_constr,' constraints on phi angles.'
1115 do i=1,ntheta_constr
1116 write (iout,'(i5,3f8.3)') itheta_constr(i),theta_constr0(i), &
1121 do i=1,ntheta_constr
1122 theta_constr0(i)=deg2rad*theta_constr0(i)
1123 theta_drange(i)=deg2rad*theta_drange(i)
1125 !C if(me.eq.king.or..not.out1file)
1126 !C & write (iout,*) 'FTORS',ftors
1127 !C do i=1,ntheta_constr
1128 !C ii = itheta_constr(i)
1129 !C thetabound(1,ii) = phi0(i)-drange(i)
1130 !C thetabound(2,ii) = phi0(i)+drange(i)
1132 endif ! ntheta_constr.gt.0
1133 endif! with_theta_constr
1137 if (me.eq.king) then
1139 write (iout,'(a)') 'Boundaries in phi angle sampling:'
1141 write (iout,'(a3,i5,2f10.1)') &
1142 restyp(itype(i,1)),i,phibound(1,i)*rad2deg,phibound(2,i)*rad2deg
1148 !d print *,'NNT=',NNT,' NCT=',NCT
1149 if (itype(1,1).eq.ntyp1) nnt=2
1150 if (itype(nres,1).eq.ntyp1) nct=nct-1
1152 if(me.eq.king.or..not.out1file) &
1153 write (iout,'(a,i3)') 'nsup=',nsup
1155 if (nsup.le.(nct-nnt+1)) then
1156 do i=0,nct-nnt+1-nsup
1157 if (seq_comp(itype(nnt+i,1),itype_pdb(nstart_sup),nsup)) then
1162 write (iout,'(a)') &
1163 'Error - sequences to be superposed do not match.'
1166 do i=0,nsup-(nct-nnt+1)
1167 if (seq_comp(itype(nnt,1),itype_pdb(nstart_sup+i),nct-nnt+1)) &
1169 nstart_sup=nstart_sup+i
1174 write (iout,'(a)') &
1175 'Error - sequences to be superposed do not match.'
1178 if (nsup.eq.0) nsup=nct-nnt
1179 if (nstart_sup.eq.0) nstart_sup=nnt
1180 if (nstart_seq.eq.0) nstart_seq=nnt
1181 if(me.eq.king.or..not.out1file) &
1182 write (iout,*) 'nsup=',nsup,' nstart_sup=',nstart_sup,&
1183 ' nstart_seq=',nstart_seq !,"242343453254"
1185 !--- Zscore rms -------
1186 if (nz_start.eq.0) nz_start=nnt
1187 if (nz_end.eq.0 .and. nsup.gt.0) then
1189 else if (nz_end.eq.0) then
1192 if(me.eq.king.or..not.out1file)then
1193 write (iout,*) 'NZ_START=',nz_start,' NZ_END=',nz_end
1194 write (iout,*) 'IZ_SC=',iz_sc
1196 !----------------------
1199 if (.not.pdbref) then
1200 call read_angles(inp,*38)
1202 38 write (iout,'(a)') 'Error reading reference structure.'
1204 call MPI_Finalize(MPI_COMM_WORLD,IERROR)
1205 stop 'Error reading reference structure'
1209 !zscore call geom_to_var(nvar,coord_exp_zs(1,1))
1216 cref(j,i,kkk)=c(j,i)
1219 call contact(.true.,ncont_ref,icont_ref,co)
1221 ! write (iout,*) "constr_dist",constr_dist,nstart_sup,nsup
1223 if (constr_dist.gt.0) call read_dist_constr
1224 write (iout,*) "After read_dist_constr nhpb",nhpb
1225 if ((AFMlog.gt.0).or.(selfguide.gt.0)) call read_afminp
1227 if(me.eq.king.or..not.out1file) &
1228 write (iout,*) 'Contact order:',co
1230 if(me.eq.king.or..not.out1file) &
1231 write (2,*) 'Shifting contacts:',nstart_seq,nstart_sup
1234 icont_ref(j,i)=icont_ref(j,i)+nstart_seq-nstart_sup
1236 if(me.eq.king.or..not.out1file) &
1237 write (2,*) i,' ',restyp(itype(icont_ref(1,i),1)),' ',&
1238 icont_ref(1,i),' ',&
1239 restyp(itype(icont_ref(2,i),1)),' ',icont_ref(2,i)
1243 if (indpdb.eq.0 .and. modecalc.ne.2 .and. modecalc.ne.4 &
1244 .and. modecalc.ne.8 .and. modecalc.ne.9 .and. &
1245 modecalc.ne.10) then
1246 ! If input structure hasn't been supplied from the PDB file read or generate
1248 if (iranconf.eq.0 .and. .not. extconf) then
1249 if(me.eq.king.or..not.out1file .and.fg_rank.eq.0) &
1250 write (iout,'(a)') 'Initial geometry will be read in.'
1252 read(inp,'(8f10.5)',end=36,err=36) &
1253 ((c(l,k),l=1,3),k=1,nres),&
1254 ((c(l,k+nres),l=1,3),k=nnt,nct)
1255 write (iout,*) "Exit READ_CART"
1256 write (iout,'(8f10.5)') &
1257 ((c(l,k),l=1,3),k=1,nres),&
1258 ((c(l,k+nres),l=1,3),k=nnt,nct)
1259 call int_from_cart1(.true.)
1260 write (iout,*) "Finish INT_TO_CART"
1263 dc(j,i)=c(j,i+1)-c(j,i)
1264 dc_norm(j,i)=dc_norm(j,i)*vbld_inv(i+1)
1268 if (itype(i,1).ne.10 .and. itype(i,1).ne.ntyp1) then
1270 dc(j,i+nres)=c(j,i+nres)-c(j,i)
1271 dc_norm(j,i+nres)=dc_norm(j,i+nres)*vbld_inv(i+nres)
1277 call read_angles(inp,*36)
1280 36 write (iout,'(a)') 'Error reading angle file.'
1282 call mpi_finalize( MPI_COMM_WORLD,IERR )
1284 stop 'Error reading angle file.'
1286 else if (extconf) then
1287 if(me.eq.king.or..not.out1file .and. fg_rank.eq.0) &
1288 write (iout,'(a)') 'Extended chain initial geometry.'
1290 theta(i)=90d0*deg2rad
1293 phi(i)=180d0*deg2rad
1296 alph(i)=110d0*deg2rad
1298 !elwrite (iout,*)"alph(i)*deg2rad",(alph(i), i=1,nres)
1300 omeg(i)=-120d0*deg2rad
1301 if (itype(i,1).le.0) omeg(i)=-omeg(i)
1304 if(me.eq.king.or..not.out1file) &
1305 write (iout,'(a)') 'Random-generated initial geometry.'
1309 if (me.eq.king .or. fg_rank.eq.0 .and. &
1310 ( modecalc.eq.12 .or. modecalc.eq.14) ) then
1314 call gen_rand_conf(itmp,*30)
1316 30 write (iout,*) 'Failed to generate random conformation',&
1318 write (*,*) 'Processor:',me,&
1319 ' Failed to generate random conformation',&
1329 write (iout,'(a,i3,a)') 'Processor:',me,&
1330 ' error in generating random conformation.'
1331 write (*,'(a,i3,a)') 'Processor:',me,&
1332 ' error in generating random conformation.'
1335 call MPI_Abort(mpi_comm_world,error_msg,ierrcode)
1341 call gen_rand_conf(itmp,*335)
1343 335 write (iout,*) 'Failed to generate random conformation',&
1345 write (*,*) 'Failed to generate random conformation',&
1348 write (iout,'(a,i3,a)') 'Processor:',me,&
1349 ' error in generating random conformation.'
1350 write (*,'(a,i3,a)') 'Processor:',me,&
1351 ' error in generating random conformation.'
1356 elseif (modecalc.eq.4) then
1357 read (inp,'(a)') intinname
1358 open (intin,file=intinname,status='old',err=333)
1359 if (me.eq.king .or. .not.out1file.and.fg_rank.eq.0) &
1360 write (iout,'(a)') 'intinname',intinname
1361 write (*,'(a)') 'Processor',myrank,' intinname',intinname
1363 333 write (iout,'(2a)') 'Error opening angle file ',intinname
1365 call MPI_Finalize(MPI_COMM_WORLD,IERR)
1367 stop 'Error opening angle file.'
1371 ! Generate distance constraints, if the PDB structure is to be regularized.
1372 if (nthread.gt.0) then
1373 call read_threadbase
1376 !elwrite (iout,*)"alph(i)*deg2rad",(alph(i), i=1,nres)
1377 if (me.eq.king .or. .not. out1file) &
1379 !elwrite (iout,*)"alph(i)*rad2deg",(alph(i)*rad2deg, i=1,nres)
1380 if (ns.gt.0 .and. (me.eq.king .or. .not.out1file) ) then
1381 write (iout,'(/a,i3,a)') &
1382 'The chain contains',ns,' disulfide-bridging cysteines.'
1383 write (iout,'(20i4)') (iss(i),i=1,ns)
1385 write(iout,*)"Running with dynamic disulfide-bond formation"
1387 write (iout,'(/a/)') 'Pre-formed links are:'
1393 if (me.eq.king.or..not.out1file) &
1394 write (iout,'(2a,i3,3a,i3,a,3f10.3)') &
1395 restyp(it1),'(',i1,') -- ',restyp(it2),'(',i2,')',dhpb(i),&
1401 if (ns.gt.0.and.dyn_ss) then
1405 forcon(i-nss)=forcon(i)
1412 dyn_ss_mask(iss(i))=.true.
1415 if (i2ndstr.gt.0) call secstrp2dihc
1416 ! call geom_to_var(nvar,x)
1417 ! call etotal(energia(0))
1418 ! call enerprint(energia(0))
1419 ! call briefout(0,etot)
1421 !d write (iout,'(2(a,i3))') 'NNT',NNT,' NCT',NCT
1422 !d write (iout,'(a)') 'Variable list:'
1423 !d write (iout,'(i4,f10.5)') (i,rad2deg*x(i),i=1,nvar)
1425 if (me.eq.king .or. (fg_rank.eq.0 .and. .not.out1file)) &
1426 write (iout,'(//80(1h*)/20x,a,i4,a/80(1h*)//)') &
1427 'Processor',myrank,': end reading molecular data.'
1430 end subroutine molread
1431 !-----------------------------------------------------------------------------
1432 !-----------------------------------------------------------------------------