8 use control_data, only:maxterm_sccor
10 !-----------------------------------------------------------------------------
11 ! Max. number of residue types and parameters in expressions for
12 ! virtual-bond angle bending potentials
13 ! integer,parameter :: maxthetyp=3
14 ! integer,parameter :: maxthetyp1=maxthetyp+1
16 ! & maxtheterm2=6,maxtheterm3=4,maxsingle=6,maxdouble=4,
17 ! & mmaxtheterm=maxtheterm)
18 !-----------------------------------------------------------------------------
19 ! Max. number of types of dihedral angles & multiplicity of torsional barriers
20 ! and the number of terms in double torsionals
21 ! integer,parameter :: maxlor=3,maxtermd_1=8,maxtermd_2=8
22 ! parameter (maxtor=4,maxterm=10)
23 !-----------------------------------------------------------------------------
24 ! Max number of torsional terms in SCCOR
25 !el integer,parameter :: maxterm_sccor=6
26 !-----------------------------------------------------------------------------
27 character(len=1),dimension(:),allocatable :: secstruc !(maxres)
28 !-----------------------------------------------------------------------------
31 !-----------------------------------------------------------------------------
33 #if .not. defined(WHAM_RUN) && .not. defined(CLUSTER)
34 !-----------------------------------------------------------------------------
36 !-----------------------------------------------------------------------------
37 subroutine write_rbank(jlee,adif,nft)
40 use geometry_data, only: nres,rad2deg
41 ! implicit real*8 (a-h,o-z)
42 ! include 'DIMENSIONS'
43 ! include 'COMMON.IOUNITS'
44 ! include 'COMMON.CSA'
45 ! include 'COMMON.BANK'
46 ! include 'COMMON.CHAIN'
47 ! include 'COMMON.GEO'
49 integer :: nft,i,k,j,l,jlee
52 open(icsa_rbank,file=csa_rbank,status="unknown")
53 write (icsa_rbank,900) jlee,nbank,nstep,nft,icycle,adif
55 write (icsa_rbank,952) k,rene(k),rrmsn(k),rpncn(k)
58 write (icsa_rbank,850) (rad2deg*rvar(i,l,j,k),i=1,4)
65 900 format (1x,"jlee =",i3,3x,"nbank =",i4,3x,"nstep =",&
67 952 format (1x,'#',i4,' total E ',1pe14.5,' rmsd from N ',0pf8.3,&
71 end subroutine write_rbank
72 !-----------------------------------------------------------------------------
73 subroutine read_rbank(jlee,adif)
76 use geometry_data, only: nres,deg2rad
78 ! implicit real*8 (a-h,o-z)
79 ! include 'DIMENSIONS'
81 ! include 'COMMON.IOUNITS'
82 ! include 'COMMON.CSA'
83 ! include 'COMMON.BANK'
84 ! include 'COMMON.CHAIN'
85 ! include 'COMMON.GEO'
86 ! include 'COMMON.SETUP'
87 character(len=80) :: karta
89 integer :: nbankr,nstepr,nftr,icycler,kk,k,j,l,i,&
90 ierror,ierrcode,jlee,jleer
93 open(icsa_rbank,file=csa_rbank,status="old")
94 read (icsa_rbank,901) jleer,nbankr,nstepr,nftr,icycler,adif
95 print *,jleer,nbankr,nstepr,nftr,icycler,adif
96 ! print *, 'adif from read_rbank ',adif
98 if(nbankr.ne.nbank) then
99 write (iout,*) 'ERROR in READ_BANK: NBANKR',nbankr,&
101 call mpi_abort(mpi_comm_world,ierror,ierrcode)
103 if(jleer.ne.jlee) then
104 write (iout,*) 'ERROR in READ_BANK: JLEER',jleer,&
106 call mpi_abort(mpi_comm_world,ierror,ierrcode)
112 read (icsa_rbank,'(a80)') karta
113 write(iout,*) "READ_RBANK: kk=",kk
115 ! if (index(karta,"*").gt.0) then
116 ! write (iout,*) "***** Stars in bankr ***** k=",k,
120 ! read (30,850) (rdummy,i=1,4)
125 call reada(karta,"total E",rene(kk),1.0d20)
126 call reada(karta,"rmsd from N",rrmsn(kk),0.0d0)
127 call reada(karta,"%NC",rpncn(kk),0.0d0)
128 write(iout,*)"total E",bene(kk),"rmsd from N",brmsn(kk),&
129 "%NC",bpncn(kk),ibank(kk)
130 ! read (icsa_rbank,953) kdummy,rene(kk),rrmsn(kk),rpncn(kk)
133 read (icsa_rbank,850) (rvar(i,l,j,kk),i=1,4)
134 ! write (iout,850) (rvar(i,l,j,kk),i=1,4)
136 rvar(i,l,j,kk)=deg2rad*rvar(i,l,j,kk)
142 !d write (*,*) "read_rbank ******************* kk",kk,
144 if (kk.lt.nbankr) nbankr=kk
149 !d write (*,850) (rvar(i,l,j,kk),i=1,4)
156 901 format (1x,6x,i3,3x,7x,i4,3x,7x,i8,i10,i2,f15.5)
157 953 format (1x,1x,i4,9x,f12.3,13x,f8.3,5x,f5.2)
160 end subroutine read_rbank
161 !-----------------------------------------------------------------------------
162 subroutine write_bank(jlee,nft)
165 use control_data, only: vdisulf
166 use geometry_data, only: nres,rad2deg
167 ! implicit real*8 (a-h,o-z)
168 ! include 'DIMENSIONS'
169 ! include 'COMMON.IOUNITS'
170 ! include 'COMMON.CSA'
171 ! include 'COMMON.BANK'
172 ! include 'COMMON.CHAIN'
173 ! include 'COMMON.GEO'
174 ! include 'COMMON.SBRIDGE'
175 ! include 'COMMON.CONTROL'
176 character(len=7) :: chtmp
177 character(len=40) :: chfrm
180 integer :: nft,k,l,i,j,jlee
182 open(icsa_bank,file=csa_bank,status="unknown")
183 write (icsa_bank,900) jlee,nbank,nstep,nft,icycle,cutdif
184 write (icsa_bank,902) nglob_csa, eglob_csa
185 open (igeom,file=intname,status='UNKNOWN')
187 write (icsa_bank,952) k,bene(k),brmsn(k),bpncn(k),ibank(k)
188 if (vdisulf) write (icsa_bank,'(101i4)') &
189 bvar_nss(k),((bvar_ss(j,i,k),j=1,2),i=1,bvar_nss(k))
192 write (icsa_bank,850) (rad2deg*bvar(i,l,j,k),i=1,4)
195 if (bvar_nss(k).le.9) then
196 write (igeom,'(I5,F10.3,I2,9(1X,2I3))') k,bene(k),&
197 bvar_nss(k),(bvar_ss(1,i,k),bvar_ss(2,i,k),i=1,bvar_nss(k))
199 write (igeom,'(I5,F10.3,I2,9(1X,2I3))') k,bene(k),&
200 bvar_nss(k),(bvar_ss(1,i,k),bvar_ss(2,i,k),i=1,9)
201 write (igeom,'(3X,11(1X,2I3))') (bvar_ss(1,i,k),&
202 bvar_ss(2,i,k),i=10,bvar_nss(k))
204 write (igeom,200) (rad2deg*bvar(1,i,1,k),i=2,nres-1)
205 write (igeom,200) (rad2deg*bvar(2,i,1,k),i=2,nres-2)
206 write (igeom,200) (rad2deg*bvar(3,i,1,k),i=2,nres-1)
207 write (igeom,200) (rad2deg*bvar(4,i,1,k),i=2,nres-1)
212 if (nstep/200.gt.ilastnstep) then
214 ilastnstep=(ilastnstep+1)*1.5
215 write(chfrm,'(a2,i1,a1)') '(i',int(dlog10(dble(nstep))+1),')'
216 write(chtmp,chfrm) nstep
217 open(icsa_int,file=prefix(:ilen(prefix)) &
218 //'_'//chtmp(:ilen(chtmp))//'.int',status='UNKNOWN')
220 if (bvar_nss(k).le.9) then
221 write (icsa_int,'(I5,F10.3,I2,9(1X,2I3))') k,bene(k),&
222 bvar_nss(k),(bvar_ss(1,i,k),bvar_ss(2,i,k),i=1,bvar_nss(k))
224 write (icsa_int,'(I5,F10.3,I2,9(1X,2I3))') k,bene(k),&
225 bvar_nss(k),(bvar_ss(1,i,k),bvar_ss(2,i,k),i=1,9)
226 write (icsa_int,'(3X,11(1X,2I3))') (bvar_ss(1,i,k),&
227 bvar_ss(2,i,k),i=10,bvar_nss(k))
229 write (icsa_int,200) (rad2deg*bvar(1,i,1,k),i=2,nres-1)
230 write (icsa_int,200) (rad2deg*bvar(2,i,1,k),i=2,nres-2)
231 write (icsa_int,200) (rad2deg*bvar(3,i,1,k),i=2,nres-1)
232 write (icsa_int,200) (rad2deg*bvar(4,i,1,k),i=2,nres-1)
240 900 format (1x,"jlee =",i3,3x,"nbank =",i4,3x,"nstep =",&
242 902 format (1x,'nglob_csa =',i4,' eglob_csa =',1pe14.5)
243 952 format (1x,'#',i4,' total E ',1pe14.5,' rmsd from N ',0pf8.3,&
247 end subroutine write_bank
248 !-----------------------------------------------------------------------------
249 subroutine write_bank_reminimized(jlee,nft)
252 use geometry_data, only: nres,rad2deg
254 ! implicit real*8 (a-h,o-z)
255 ! include 'DIMENSIONS'
256 ! include 'COMMON.IOUNITS'
257 ! include 'COMMON.CSA'
258 ! include 'COMMON.BANK'
259 ! include 'COMMON.CHAIN'
260 ! include 'COMMON.GEO'
261 ! include 'COMMON.SBRIDGE'
263 integer :: nft,i,l,j,k,jlee
265 open(icsa_bank_reminimized,file=csa_bank_reminimized,&
267 write (icsa_bank_reminimized,900) &
268 jlee,nbank,nstep,nft,icycle,cutdif
269 open (igeom,file=intname,status='UNKNOWN')
271 write (icsa_bank_reminimized,952) k,bene(k),brmsn(k),&
275 write (icsa_bank_reminimized,850) (rad2deg*bvar(i,l,j,k),i=1,4)
279 write (igeom,'(I5,F10.3,I2,9(1X,2I3))') k,bene(k),&
280 nss,(ihpb(i),jhpb(i),i=1,nss)
282 write (igeom,'(I5,F10.3,I2,9(1X,2I3))') k,bene(k),&
283 nss,(ihpb(i),jhpb(i),i=1,9)
284 write (igeom,'(3X,11(1X,2I3))') (ihpb(i),jhpb(i),i=10,nss)
286 write (igeom,200) (rad2deg*bvar(1,i,1,k),i=2,nres-1)
287 write (igeom,200) (rad2deg*bvar(2,i,1,k),i=2,nres-2)
288 write (igeom,200) (rad2deg*bvar(3,i,1,k),i=2,nres-1)
289 write (igeom,200) (rad2deg*bvar(4,i,1,k),i=2,nres-1)
291 close(icsa_bank_reminimized)
296 900 format (1x,"jlee =",i3,3x,"nbank =",i4,3x,"nstep =",&
298 952 format (1x,'#',i4,' total E ',1pe14.5,' rmsd from N ',0pf8.3,&
302 end subroutine write_bank_reminimized
303 !-----------------------------------------------------------------------------
304 subroutine read_bank(jlee,nft,cutdifr)
307 use control_data, only: vdisulf
308 use geometry_data, only: nres,deg2rad
310 ! implicit real*8 (a-h,o-z)
311 ! include 'DIMENSIONS'
312 ! include 'COMMON.IOUNITS'
313 ! include 'COMMON.CSA'
314 ! include 'COMMON.BANK'
315 ! include 'COMMON.CHAIN'
316 ! include 'COMMON.GEO'
317 ! include 'COMMON.CONTROL'
318 ! include 'COMMON.SBRIDGE'
319 character(len=80) :: karta
323 integer :: nft,kk,k,l,i,j,jlee
324 real(kind=8) :: cutdifr
326 open(icsa_bank,file=csa_bank,status="old")
327 read (icsa_bank,901) jlee,nbank,nstep,nft,icycle,cutdifr
328 read (icsa_bank,902) nglob_csa, eglob_csa
329 ! if(jleer.ne.jlee) then
330 ! write (iout,*) 'ERROR in READ_BANK: JLEER',jleer,
332 ! call mpi_abort(mpi_comm_world,ierror,ierrcode)
337 read (icsa_bank,'(a80)') karta
338 write(iout,*) "READ_BANK: kk=",kk
340 ! if (index(karta,"*").gt.0) then
341 ! write (iout,*) "***** Stars in bank ***** k=",k,
345 ! read (33,850) (rdummy,i=1,4)
350 call reada(karta,"total E",bene(kk),1.0d20)
351 call reada(karta,"rmsd from N",brmsn(kk),0.0d0)
352 call reada(karta,"%NC",bpncn(kk),0.0d0)
353 read (karta(ilen(karta)-1:),*,end=111,err=111) ibank(kk)
357 write(iout,*)"total E",bene(kk),"rmsd from N",brmsn(kk),&
358 "%NC",bpncn(kk),ibank(kk)
359 ! read (icsa_bank,953) kdummy,bene(k),brmsn(k),bpncn(k),ibank(k)
361 read (icsa_bank,'(101i4)') &
362 bvar_nss(kk),((bvar_ss(j,i,kk),j=1,2),i=1,bvar_nss(kk))
363 bvar_ns(kk)=ns-2*bvar_nss(kk)
364 write(iout,*) 'read SSBOND',bvar_nss(kk),&
365 ((bvar_ss(j,i,kk),j=1,2),i=1,bvar_nss(kk))
366 !d write(iout,*) 'read CYS #free ', bvar_ns(kk)
370 do while( iss(i).ne.bvar_ss(1,j,kk)-nres .and. &
371 iss(i).ne.bvar_ss(2,j,kk)-nres .and. &
375 if (j.gt.bvar_nss(kk)) then
380 !d write(iout,*)'read CYS free',(bvar_s(l,kk),l=1,bvar_ns(kk))
384 read (icsa_bank,850) (bvar(i,l,j,kk),i=1,4)
385 ! write (iout,850) (bvar(i,l,j,kk),i=1,4)
387 bvar(i,l,j,kk)=deg2rad*bvar(i,l,j,kk)
394 if (kk.lt.nbank) nbank=kk
395 !d write (*,*) "read_bank ******************* kk",kk,
401 !d write (*,850) (bvar(i,l,j,kk),i=1,4)
407 ! read (33,953) kdummy,bene(k),brmsn(k),bpncn(k),ibank(k)
410 ! read (33,850) (bvar(i,l,j,k),i=1,4)
412 ! bvar(i,l,j,k)=deg2rad*bvar(i,l,j,k)
420 952 format (1x,'#',i4,' total E ',f12.3,' rmsd from N ',f8.3,i5)
421 901 format (1x,6x,i3,3x,7x,i4,3x,7x,i8,i10,i2,f15.5)
422 902 format (1x,11x,i4,12x,1pe14.5)
423 953 format (1x,1x,i4,9x,f12.3,13x,f8.3,5x,f5.2,i5)
426 end subroutine read_bank
427 !-----------------------------------------------------------------------------
428 subroutine write_bank1(jlee)
431 use geometry_data, only: nres,rad2deg
432 ! implicit real*8 (a-h,o-z)
433 ! include 'DIMENSIONS'
434 ! include 'COMMON.IOUNITS'
435 ! include 'COMMON.CSA'
436 ! include 'COMMON.BANK'
437 ! include 'COMMON.CHAIN'
438 ! include 'COMMON.GEO'
440 integer :: k,i,l,j,jlee
442 #if defined(AIX) || defined(PGI)
443 open(icsa_bank1,file=csa_bank1,position="append")
445 open(icsa_bank1,file=csa_bank1,access="append")
447 write (icsa_bank1,900) jlee,nbank,nstep,cutdif
449 write (icsa_bank1,952) k,bene(k),brmsn(k),bpncn(k),ibank(k)
452 write (icsa_bank1,850) (rad2deg*bvar(i,l,j,k),i=1,4)
458 900 format (4x,"jlee =",i5,3x,"nbank =",i5,3x,"nstep =",i10,f15.5)
459 952 format (1x,'#',i4,' total E ',1pe14.5,' rmsd from N ',0pf8.3,&
463 end subroutine write_bank1
464 !-----------------------------------------------------------------------------
466 !-----------------------------------------------------------------------------
467 ! subroutine cartprint
469 ! use geometry_data, only: c
470 ! use energy_data, only: itype
471 ! implicit real*8 (a-h,o-z)
472 ! include 'DIMENSIONS'
473 ! include 'COMMON.CHAIN'
474 ! include 'COMMON.INTERACT'
475 ! include 'COMMON.NAMES'
476 ! include 'COMMON.IOUNITS'
481 ! write (iout,110) restyp(itype(i,1)),i,c(1,i),c(2,i),&
482 ! c(3,i),c(1,nres+i),c(2,nres+i),c(3,nres+i)
484 ! 100 format (//' alpha-carbon coordinates ',&
485 ! ' centroid coordinates'/ &
486 ! ' ', 6X,'X',11X,'Y',11X,'Z',&
487 ! 10X,'X',11X,'Y',11X,'Z')
488 ! 110 format (a,'(',i3,')',6f12.5)
490 ! end subroutine cartprint
491 !-----------------------------------------------------------------------------
493 !-----------------------------------------------------------------------------
494 subroutine secstrp2dihc
498 ! implicit real*8 (a-h,o-z)
499 ! include 'DIMENSIONS'
500 ! include 'COMMON.GEO'
501 ! include 'COMMON.BOUNDS'
502 ! include 'COMMON.CHAIN'
503 ! include 'COMMON.TORCNSTR'
504 ! include 'COMMON.IOUNITS'
505 !el character(len=1),dimension(nres) :: secstruc !(maxres)
506 !el COMMON/SECONDARYS/secstruc
507 character(len=80) :: line
512 integer :: i,ii,lenpre
514 allocate(secstruc(nres))
516 !dr call getenv_loc('SECPREDFIL',secpred)
518 secpred=prefix(:lenpre)//'.spred'
520 #if defined(WINIFL) || defined(WINPGI)
521 open(isecpred,file=secpred,status='old',readonly,shared)
522 #elif (defined CRAY) || (defined AIX)
523 open(isecpred,file=secpred,status='old',action='read')
525 open(isecpred,file=secpred,status='old')
527 open(isecpred,file=secpred,status='old',action='read')
529 ! read secondary structure prediction from JPRED here!
530 ! read(isecpred,'(A80)',err=100,end=100) line
531 ! read(line,'(f10.3)',err=110) ftors
532 read(isecpred,'(f10.3)',err=110) ftors(1)
534 write (iout,*) 'FTORS factor =',ftors(1)
535 ! initialize secstruc to any
542 call read_secstr_pred(isecpred,iout,errflag)
544 write(iout,*)'There is a problem with the list of secondary-',&
545 'structure prediction'
548 ! 8/13/98 Set limits to generating the dihedral angles
557 if ( secstruc(i) .eq. 'H') then
558 ! Helix restraints for this residue
561 phi0(ii) = 45.0D0*deg2rad
562 drange(ii)= 5.0D0*deg2rad
563 phibound(1,i) = phi0(ii)-drange(ii)
564 phibound(2,i) = phi0(ii)+drange(ii)
565 else if (secstruc(i) .eq. 'E') then
566 ! strand restraints for this residue
569 phi0(ii) = 180.0D0*deg2rad
570 drange(ii)= 5.0D0*deg2rad
571 phibound(1,i) = phi0(ii)-drange(ii)
572 phibound(2,i) = phi0(ii)+drange(ii)
574 ! no restraints for this residue
575 ndih_nconstr=ndih_nconstr+1
576 idih_nconstr(ndih_nconstr)=i
580 ! deallocate(secstruc)
583 write(iout,'(A30,A80)')'Error reading file SECPRED',secpred
584 ! deallocate(secstruc)
587 write(iout,'(A20)')'Error reading FTORS'
588 ! deallocate(secstruc)
590 end subroutine secstrp2dihc
591 !-----------------------------------------------------------------------------
592 subroutine read_secstr_pred(jin,jout,errors)
594 ! implicit real*8 (a-h,o-z)
595 ! INCLUDE 'DIMENSIONS'
596 ! include 'COMMON.IOUNITS'
597 ! include 'COMMON.CHAIN'
598 !el character(len=1),dimension(nres) :: secstruc !(maxres)
599 !el COMMON/SECONDARYS/secstruc
601 character(len=80) :: line,line1 !,ucase
602 logical :: errflag,errors,blankline
605 integer :: jin,jout,iseq,ipos,ipos1,iend,il,&
608 read (jin,'(a)') line
609 write (jout,'(2a)') '> ',line(1:78)
611 ! Remember that we number full residues starting from 2, then, iseq=1 and iseq=nres
612 ! correspond to the end-groups. ADD to the secondary structure prediction "-" for the
613 ! end-groups in the input file "*.spred"
616 do while (index(line1,'$END').eq.0)
617 ! Override commented lines.
620 do while (.not.blankline)
622 call mykey(line,line1,ipos,blankline,errflag)
623 if (errflag) write (jout,'(2a)') &
624 'Error when reading sequence in line: ',line
625 errors=errors .or. errflag
626 if (.not. blankline .and. .not. errflag) then
629 !el if (iseq.le.maxres) then
630 if (line1(1:1).eq.'-' ) then
631 secstruc(iseq)=line1(1:1)
632 else if ( ( ucase(line1(1:1)).eq.'E' ) .or. &
633 ( ucase(line1(1:1)).eq.'H' ) ) then
634 secstruc(iseq)=ucase(line1(1:1))
637 write (jout,1010) line1(1:1), iseq
642 !el write (jout,1000) iseq,maxres
645 do while (ipos1.le.iend)
650 !el if (iseq.le.maxres) then
651 if (line1(ipos1-1:ipos1-1).eq.'-' ) then
652 secstruc(iseq)=line1(ipos1-1:ipos1-1)
653 else if((ucase(line1(ipos1-1:ipos1-1)).eq.'E').or. &
654 (ucase(line1(ipos1-1:ipos1-1)).eq.'H') ) then
655 secstruc(iseq)=ucase(line1(ipos1-1:ipos1-1))
658 write (jout,1010) line1(ipos1-1:ipos1-1), iseq
663 !el write (jout,1000) iseq,maxres
670 read (jin,'(a)') line
671 write (jout,'(2a)') '> ',line(1:78)
675 !d write (jout,'(10a8)') (sequence(i),i=1,iseq-1)
677 !d check whether the found length of the chain is correct.
678 length_of_chain=iseq-1
679 if (length_of_chain .ne. nres) then
681 write (jout,'(a,i4,a,i4,a)') &
682 'Error: the number of labels specified in $SEC_STRUC_PRED (' &
683 ,length_of_chain,') does not match with the number of residues (' &
688 1000 format('Error - the number of residues (',i4,&
689 ') has exceeded maximum (',i4,').')
690 1010 format ('Error - unrecognized secondary structure label',a4,&
693 end subroutine read_secstr_pred
695 !-----------------------------------------------------------------------------
697 !-----------------------------------------------------------------------------
702 use control_data, only:maxterm !,maxtor
706 use control, only: getenv_loc
708 ! Read the parameters of the probability distributions of the virtual-bond
709 ! valence angles and the side chains and energy parameters.
711 ! Important! Energy-term weights ARE NOT read here; they are read from the
712 ! main input file instead, because NO defaults have yet been set for these
715 ! implicit real*8 (a-h,o-z)
716 ! include 'DIMENSIONS'
721 ! include 'COMMON.IOUNITS'
722 ! include 'COMMON.CHAIN'
723 ! include 'COMMON.INTERACT'
724 ! include 'COMMON.GEO'
725 ! include 'COMMON.LOCAL'
726 ! include 'COMMON.TORSION'
727 ! include 'COMMON.SCCOR'
728 ! include 'COMMON.SCROT'
729 ! include 'COMMON.FFIELD'
730 ! include 'COMMON.NAMES'
731 ! include 'COMMON.SBRIDGE'
732 ! include 'COMMON.MD'
733 ! include 'COMMON.SETUP'
734 character(len=1) :: t1,t2,t3
735 character(len=1) :: onelett(4) = (/"G","A","P","D"/)
736 character(len=1) :: toronelet(-2:2) = (/"p","a","G","A","P"/)
737 logical :: lprint,LaTeX,SPLIT_FOURIERTOR
738 real(kind=8),dimension(3,3,maxlob) :: blower !(3,3,maxlob)
739 real(kind=8),dimension(13) :: buse
740 character(len=3) :: lancuch !,ucase
742 integer :: m,n,l,i,j,k,iblock,lll,llll,ll,nlobi,mm,jj
743 integer :: maxinter,junk,kk,ii,ncatprotparm,nkcctyp
744 real(kind=8) :: v0ijsccor,v0ijsccor1,v0ijsccor2,v0ijsccor3,si,&
745 dwa16,rjunk,akl,v0ij,rri,epsij,rrij,sigeps,sigt1sq,&
746 sigt2sq,sigii1,sigii2,ratsig1,ratsig2,rsum_max,r_augm,&
747 res1,epsijlip,epspeptube,epssctube,sigmapeptube, &
749 integer :: ichir1,ichir2,ijunk
752 ! real(kind=8),dimension(maxterm,-maxtor:maxtor,-maxtor:maxtor,2) :: v1_el,v2_el !(maxterm,-maxtor:maxtor,-maxtor:maxtor,2)
753 !el allocate(v1_el(maxterm,-maxtor:maxtor,-maxtor:maxtor,2))
754 !el allocate(v2_el(maxterm,-maxtor:maxtor,-maxtor:maxtor,2))
756 ! For printing parameters after they are read set the following in the UNRES
759 ! setenv PRINT_PARM YES
761 ! To print parameters in LaTeX format rather than as ASCII tables:
765 call getenv_loc("PRINT_PARM",lancuch)
766 lprint = (ucase(lancuch).eq."YES" .or. ucase(lancuch).eq."Y")
767 call getenv_loc("LATEX",lancuch)
768 LaTeX = (ucase(lancuch).eq."YES" .or. ucase(lancuch).eq."Y")
770 dwa16=2.0d0**(1.0d0/6.0d0)
772 ! Assign virtual-bond length
775 vblinv2=vblinv*vblinv
777 ! Read the virtual-bond parameters, masses, and moments of inertia
778 ! and Stokes' radii of the peptide group and side chains
780 allocate(dsc(ntyp1)) !(ntyp1)
781 allocate(dsc_inv(ntyp1)) !(ntyp1)
782 allocate(nbondterm_nucl(ntyp_molec(2))) !(ntyp)
783 allocate(vbldsc0_nucl(maxbondterm,ntyp_molec(2))) !(maxbondterm,ntyp)
784 allocate(aksc_nucl(maxbondterm,ntyp_molec(2))) !(maxbondterm,ntyp)
785 allocate(nbondterm(ntyp)) !(ntyp)
786 allocate(vbldsc0(maxbondterm,ntyp)) !(maxbondterm,ntyp)
787 allocate(aksc(maxbondterm,ntyp)) !(maxbondterm,ntyp)
788 allocate(abond0(maxbondterm,ntyp)) !(maxbondterm,ntyp)
789 allocate(long_r_sidechain(ntyp))
790 allocate(short_r_sidechain(ntyp))
795 allocate(msc(ntyp+1)) !(ntyp+1)
796 allocate(isc(ntyp+1)) !(ntyp+1)
797 allocate(restok(ntyp+1)) !(ntyp+1)
799 read (ibond,*) vbldp0,akp,mp,ip,pstok
802 read (ibond,*) vbldsc0(1,i),aksc(1,i),msc(i),isc(i),restok(i)
803 dsc(i) = vbldsc0(1,i)
807 dsc_inv(i)=1.0D0/dsc(i)
816 allocate(msc(ntyp+1,5)) !(ntyp+1)
817 allocate(isc(ntyp+1,5)) !(ntyp+1)
818 allocate(restok(ntyp+1,5)) !(ntyp+1)
820 read (ibond,*) junk,vbldp0,vbldpDUM,akp,rjunk,mp(1),ip(1),pstok(1)
822 read (ibond,*) nbondterm(i),(vbldsc0(j,i),aksc(j,i),abond0(j,i),&
823 j=1,nbondterm(i)),msc(i,1),isc(i,1),restok(i,1)
824 dsc(i) = vbldsc0(1,i)
828 dsc_inv(i)=1.0D0/dsc(i)
832 read (ibond_nucl,*) vbldp0_nucl,akp_nucl,mp(2),ip(2),pstok(2)
835 read (ibond_nucl,*) vbldsc0_nucl(1,i),aksc_nucl(1,i),msc(i,2),isc(i,2),restok(i,2)
836 ! dsc(i) = vbldsc0_nucl(1,i)
840 ! dsc_inv(i)=1.0D0/dsc(i)
843 ! read (ibond_nucl,*) junk,vbldp0_nucl,akp_nucl,rjunk,mp(2),ip(2),pstok(2)
844 ! do i=1,ntyp_molec(2)
845 ! read (ibond_nucl,*) nbondterm_nucl(i),(vbldsc0_nucl(j,i),&
846 ! aksc_nucl(j,i),abond0_nucl(j,i),&
847 ! j=1,nbondterm_nucl(i)),msc(i,2),isc(i,2),restok(i,2)
848 ! dsc(i) = vbldsc0(1,i)
852 ! dsc_inv(i)=1.0D0/dsc(i)
857 write(iout,'(/a/)')"Dynamic constants of the interaction sites:"
858 write (iout,'(a10,a3,6a10)') 'Type','N','VBL','K','A0','mass',&
860 write(iout,'(a10,i3,6f10.5)') "p",1,vbldp0,akp,0.0d0,mp(1),ip(1),pstok(1)
862 write (iout,'(a10,i3,6f10.5)') restyp(i,1),nbondterm(i),&
863 vbldsc0(1,i),aksc(1,i),abond0(1,i),msc(i,1),isc(i,1),restok(i,1)
865 write (iout,'(13x,3f10.5)') &
866 vbldsc0(j,i),aksc(j,i),abond0(j,i)
870 if (oldion.eq.1) then
872 read(iion,*) msc(i,5),restok(i,5)
873 print *,msc(i,5),restok(i,5)
877 read (iion,*) ncatprotparm
878 allocate(catprm(ncatprotparm,4))
880 read (iion,*) (catprm(i,k),i=1,ncatprotparm)
884 ! read (iion,*) (vcatprm(k),k=1,ncatprotpram)
885 !----------------------------------------------------
886 allocate(a0thet(-ntyp:ntyp),theta0(-ntyp:ntyp))
887 allocate(sig0(-ntyp:ntyp),sigc0(-ntyp:ntyp)) !(-ntyp:ntyp)
888 allocate(athet(2,-ntyp:ntyp,-1:1,-1:1))
889 allocate(bthet(2,-ntyp:ntyp,-1:1,-1:1)) !(2,-ntyp:ntyp,-1:1,-1:1)
890 allocate(polthet(0:3,-ntyp:ntyp)) !(0:3,-ntyp:ntyp)
891 allocate(gthet(3,-ntyp:ntyp)) !(3,-ntyp:ntyp)
901 allocate(liptranene(ntyp))
902 !C reading lipid parameters
903 write (iout,*) "iliptranpar",iliptranpar
905 read(iliptranpar,*) pepliptran
908 read(iliptranpar,*) liptranene(i)
909 print *,liptranene(i)
915 ! Read the parameters of the probability distribution/energy expression
916 ! of the virtual-bond valence angles theta
919 read (ithep,*,err=111,end=111) a0thet(i),(athet(j,i,1,1),j=1,2),&
920 (bthet(j,i,1,1),j=1,2)
921 read (ithep,*,err=111,end=111) (polthet(j,i),j=0,3)
922 read (ithep,*,err=111,end=111) (gthet(j,i),j=1,3)
923 read (ithep,*,err=111,end=111) theta0(i),sig0(i),sigc0(i)
927 athet(1,i,1,-1)=athet(1,i,1,1)
928 athet(2,i,1,-1)=athet(2,i,1,1)
929 bthet(1,i,1,-1)=-bthet(1,i,1,1)
930 bthet(2,i,1,-1)=-bthet(2,i,1,1)
931 athet(1,i,-1,1)=-athet(1,i,1,1)
932 athet(2,i,-1,1)=-athet(2,i,1,1)
933 bthet(1,i,-1,1)=bthet(1,i,1,1)
934 bthet(2,i,-1,1)=bthet(2,i,1,1)
938 athet(1,i,-1,-1)=athet(1,-i,1,1)
939 athet(2,i,-1,-1)=-athet(2,-i,1,1)
940 bthet(1,i,-1,-1)=bthet(1,-i,1,1)
941 bthet(2,i,-1,-1)=-bthet(2,-i,1,1)
942 athet(1,i,-1,1)=athet(1,-i,1,1)
943 athet(2,i,-1,1)=-athet(2,-i,1,1)
944 bthet(1,i,-1,1)=-bthet(1,-i,1,1)
945 bthet(2,i,-1,1)=bthet(2,-i,1,1)
946 athet(1,i,1,-1)=-athet(1,-i,1,1)
947 athet(2,i,1,-1)=athet(2,-i,1,1)
948 bthet(1,i,1,-1)=bthet(1,-i,1,1)
949 bthet(2,i,1,-1)=-bthet(2,-i,1,1)
954 polthet(j,i)=polthet(j,-i)
957 gthet(j,i)=gthet(j,-i)
965 'Parameters of the virtual-bond valence angles:'
966 write (iout,'(/a/9x,5a/79(1h-))') 'Fourier coefficients:',&
967 ' ATHETA0 ',' A1 ',' A2 ',&
970 write(iout,'(a3,i4,2x,5(1pe14.5))') restyp(i,1),i,&
971 a0thet(i),(athet(j,i,1,1),j=1,2),(bthet(j,i,1,1),j=1,2)
973 write (iout,'(/a/9x,5a/79(1h-))') &
974 'Parameters of the expression for sigma(theta_c):',&
975 ' ALPH0 ',' ALPH1 ',' ALPH2 ',&
976 ' ALPH3 ',' SIGMA0C '
978 write (iout,'(a3,i4,2x,5(1pe14.5))') restyp(i,1),i,&
979 (polthet(j,i),j=0,3),sigc0(i)
981 write (iout,'(/a/9x,5a/79(1h-))') &
982 'Parameters of the second gaussian:',&
983 ' THETA0 ',' SIGMA0 ',' G1 ',&
986 write (iout,'(a3,i4,2x,5(1pe14.5))') restyp(i,1),i,theta0(i),&
987 sig0(i),(gthet(j,i),j=1,3)
991 'Parameters of the virtual-bond valence angles:'
992 write (iout,'(/a/9x,5a/79(1h-))') &
993 'Coefficients of expansion',&
994 ' theta0 ',' a1*10^2 ',' a2*10^2 ',&
995 ' b1*10^1 ',' b2*10^1 '
997 write(iout,'(a3,1h&,2x,5(f8.3,1h&))') restyp(i,1),&
998 a0thet(i),(100*athet(j,i,1,1),j=1,2),&
999 (10*bthet(j,i,1,1),j=1,2)
1001 write (iout,'(/a/9x,5a/79(1h-))') &
1002 'Parameters of the expression for sigma(theta_c):',&
1003 ' alpha0 ',' alph1 ',' alph2 ',&
1004 ' alhp3 ',' sigma0c '
1006 write (iout,'(a3,1h&,2x,5(1pe12.3,1h&))') restyp(i,1),&
1007 (polthet(j,i),j=0,3),sigc0(i)
1009 write (iout,'(/a/9x,5a/79(1h-))') &
1010 'Parameters of the second gaussian:',&
1011 ' theta0 ',' sigma0*10^2 ',' G1*10^-1',&
1014 write (iout,'(a3,1h&,2x,5(f8.3,1h&))') restyp(i,1),theta0(i),&
1015 100*sig0(i),gthet(1,i)*0.1D0,gthet(2,i),gthet(3,i)*10.0D0
1021 ! Read the parameters of Utheta determined from ab initio surfaces
1022 ! Kozlowska et al., J. Phys.: Condens. Matter 19 (2007) 285203
1024 IF (tor_mode.eq.0) THEN
1025 read (ithep,*,err=111,end=111) nthetyp,ntheterm,ntheterm2,&
1026 ntheterm3,nsingle,ndouble
1027 nntheterm=max0(ntheterm,ntheterm2,ntheterm3)
1029 !----------------------------------------------------
1030 allocate(ithetyp(-ntyp1:ntyp1)) !(-ntyp1:ntyp1)
1031 allocate(aa0thet(-nthetyp-1:nthetyp+1,&
1032 -nthetyp-1:nthetyp+1,-nthetyp-1:nthetyp+1,2))
1033 !(-maxthetyp1:maxthetyp1,-maxthetyp1:maxthetyp1,-maxthetyp1:maxthetyp1,2)
1034 allocate(aathet(ntheterm,-nthetyp-1:nthetyp+1,&
1035 -nthetyp-1:nthetyp+1,-nthetyp-1:nthetyp+1,2))
1036 !(maxtheterm,-maxthetyp1:maxthetyp1,&
1037 ! -maxthetyp1:maxthetyp1,-maxthetyp1:maxthetyp1,2)
1038 allocate(bbthet(nsingle,ntheterm2,-nthetyp-1:nthetyp+1,&
1039 -nthetyp-1:nthetyp+1,-nthetyp-1:nthetyp+1,2))
1040 allocate(ccthet(nsingle,ntheterm2,-nthetyp-1:nthetyp+1,&
1041 -nthetyp-1:nthetyp+1,-nthetyp-1:nthetyp+1,2))
1042 allocate(ddthet(nsingle,ntheterm2,-nthetyp-1:nthetyp+1,&
1043 -nthetyp-1:nthetyp+1,-nthetyp-1:nthetyp+1,2))
1044 allocate(eethet(nsingle,ntheterm2,-nthetyp-1:nthetyp+1,&
1045 -nthetyp-1:nthetyp+1,-nthetyp-1:nthetyp+1,2))
1046 !(maxsingle,maxtheterm2,-maxthetyp1:maxthetyp1,&
1047 ! -maxthetyp1:maxthetyp1,-maxthetyp1:maxthetyp1,2)
1048 allocate(ffthet(ndouble,ndouble,ntheterm3,-nthetyp-1:nthetyp+1,&
1049 -nthetyp-1:nthetyp+1,-nthetyp-1:nthetyp+1,2))
1050 allocate(ggthet(ndouble,ndouble,ntheterm3,-nthetyp-1:nthetyp+1,&
1051 -nthetyp-1:nthetyp+1,-nthetyp-1:nthetyp+1,2))
1052 !(maxdouble,maxdouble,maxtheterm3,-maxthetyp1:maxthetyp1,&
1053 ! -maxthetyp1:maxthetyp1,-maxthetyp1:maxthetyp1,2))
1055 read (ithep,*,err=111,end=111) (ithetyp(i),i=1,ntyp1)
1057 ithetyp(i)=-ithetyp(-i)
1060 aa0thet(:,:,:,:)=0.0d0
1061 aathet(:,:,:,:,:)=0.0d0
1062 bbthet(:,:,:,:,:,:)=0.0d0
1063 ccthet(:,:,:,:,:,:)=0.0d0
1064 ddthet(:,:,:,:,:,:)=0.0d0
1065 eethet(:,:,:,:,:,:)=0.0d0
1066 ffthet(:,:,:,:,:,:,:)=0.0d0
1067 ggthet(:,:,:,:,:,:,:)=0.0d0
1069 ! VAR:iblock means terminally blocking group 1=non-proline 2=proline
1071 ! VAR:ntethtyp is type of theta potentials type currently 0=glycine
1072 ! VAR:1=non-glicyne non-proline 2=proline
1073 ! VAR:negative values for D-aminoacid
1075 do j=-nthetyp,nthetyp
1076 do k=-nthetyp,nthetyp
1077 read (ithep,'(6a)',end=111,err=111) res1
1078 read (ithep,*,end=111,err=111) aa0thet(i,j,k,iblock)
1079 ! VAR: aa0thet is variable describing the average value of Foureir
1080 ! VAR: expansion series
1081 ! VAR: aathet is foureir expansion in theta/2 angle for full formula
1082 ! VAR: look at the fitting equation in Kozlowska et al., J. Phys.:
1083 !ondens. Matter 19 (2007) 285203 and Sieradzan et al., unpublished
1084 read (ithep,*,end=111,err=111) &
1085 (aathet(l,i,j,k,iblock),l=1,ntheterm)
1086 read (ithep,*,end=111,err=111) &
1087 ((bbthet(lll,ll,i,j,k,iblock),lll=1,nsingle),&
1088 (ccthet(lll,ll,i,j,k,iblock),lll=1,nsingle),&
1089 (ddthet(lll,ll,i,j,k,iblock),lll=1,nsingle),&
1090 (eethet(lll,ll,i,j,k,iblock),lll=1,nsingle),&
1092 read (ithep,*,end=111,err=111) &
1093 (((ffthet(llll,lll,ll,i,j,k,iblock),&
1094 ffthet(lll,llll,ll,i,j,k,iblock),&
1095 ggthet(llll,lll,ll,i,j,k,iblock),&
1096 ggthet(lll,llll,ll,i,j,k,iblock),&
1097 llll=1,lll-1),lll=2,ndouble),ll=1,ntheterm3)
1102 ! For dummy ends assign glycine-type coefficients of theta-only terms; the
1103 ! coefficients of theta-and-gamma-dependent terms are zero.
1104 ! IF YOU WANT VALENCE POTENTIALS FOR DUMMY ATOM UNCOMENT BELOW (NOT
1105 ! RECOMENTDED AFTER VERSION 3.3)
1109 ! aathet(l,i,j,nthetyp+1,iblock)=aathet(l,i,j,1,iblock)
1110 ! aathet(l,nthetyp+1,i,j,iblock)=aathet(l,1,i,j,iblock)
1112 ! aa0thet(i,j,nthetyp+1,iblock)=aa0thet(i,j,1,iblock)
1113 ! aa0thet(nthetyp+1,i,j,iblock)=aa0thet(1,i,j,iblock)
1116 ! aathet(l,nthetyp+1,i,nthetyp+1,iblock)=aathet(l,1,i,1,iblock)
1118 ! aa0thet(nthetyp+1,i,nthetyp+1,iblock)=aa0thet(1,i,1,iblock)
1121 ! AND COMMENT THE LOOPS BELOW
1125 aathet(l,i,j,nthetyp+1,iblock)=0.0d0
1126 aathet(l,nthetyp+1,i,j,iblock)=0.0d0
1128 aa0thet(i,j,nthetyp+1,iblock)=0.0d0
1129 aa0thet(nthetyp+1,i,j,iblock)=0.0d0
1132 aathet(l,nthetyp+1,i,nthetyp+1,iblock)=0.0d0
1134 aa0thet(nthetyp+1,i,nthetyp+1,iblock)=0.0d0
1139 ! Substitution for D aminoacids from symmetry.
1142 do j=-nthetyp,nthetyp
1143 do k=-nthetyp,nthetyp
1144 aa0thet(i,j,k,iblock)=aa0thet(-i,-j,-k,iblock)
1146 aathet(l,i,j,k,iblock)=aathet(l,-i,-j,-k,iblock)
1150 bbthet(lll,ll,i,j,k,iblock)=bbthet(lll,ll,-i,-j,-k,iblock)
1151 ccthet(lll,ll,i,j,k,iblock)=-ccthet(lll,ll,-i,-j,-k,iblock)
1152 ddthet(lll,ll,i,j,k,iblock)=ddthet(lll,ll,-i,-j,-k,iblock)
1153 eethet(lll,ll,i,j,k,iblock)=-eethet(lll,ll,-i,-j,-k,iblock)
1159 ffthet(llll,lll,ll,i,j,k,iblock)= &
1160 ffthet(llll,lll,ll,-i,-j,-k,iblock)
1161 ffthet(lll,llll,ll,i,j,k,iblock)= &
1162 ffthet(lll,llll,ll,-i,-j,-k,iblock)
1163 ggthet(llll,lll,ll,i,j,k,iblock)= &
1164 -ggthet(llll,lll,ll,-i,-j,-k,iblock)
1165 ggthet(lll,llll,ll,i,j,k,iblock)= &
1166 -ggthet(lll,llll,ll,-i,-j,-k,iblock)
1175 ! Control printout of the coefficients of virtual-bond-angle potentials
1178 write (iout,'(//a)') 'Parameter of virtual-bond-angle potential'
1183 write (iout,'(//4a)') &
1184 'Type ',onelett(i),onelett(j),onelett(k)
1185 write (iout,'(//a,10x,a)') " l","a[l]"
1186 write (iout,'(i2,1pe15.5)') 0,aa0thet(i,j,k,iblock)
1187 write (iout,'(i2,1pe15.5)') &
1188 (l,aathet(l,i,j,k,iblock),l=1,ntheterm)
1190 write (iout,'(//2h m,4(9x,a,3h[m,,i1,1h]))') &
1191 "b",l,"c",l,"d",l,"e",l
1193 write (iout,'(i2,4(1pe15.5))') m,&
1194 bbthet(m,l,i,j,k,iblock),ccthet(m,l,i,j,k,iblock),&
1195 ddthet(m,l,i,j,k,iblock),eethet(m,l,i,j,k,iblock)
1199 write (iout,'(//3hm,n,4(6x,a,5h[m,n,,i1,1h]))') &
1200 "f+",l,"f-",l,"g+",l,"g-",l
1203 write (iout,'(i1,1x,i1,4(1pe15.5))') n,m,&
1204 ffthet(n,m,l,i,j,k,iblock),&
1205 ffthet(m,n,l,i,j,k,iblock),&
1206 ggthet(n,m,l,i,j,k,iblock),&
1207 ggthet(m,n,l,i,j,k,iblock)
1218 !C here will be the apropriate recalibrating for D-aminoacid
1219 read (ithep,*,end=121,err=121) nthetyp
1220 allocate(nbend_kcc_Tb(-nthetyp:nthetyp))
1221 allocate(v1bend_chyb(0:36,-nthetyp:nthetyp))
1222 do i=-nthetyp+1,nthetyp-1
1223 read (ithep,*,end=121,err=121) nbend_kcc_Tb(i)
1224 do j=0,nbend_kcc_Tb(i)
1225 read (ithep,*,end=121,err=121) ijunk,v1bend_chyb(j,i)
1229 write (iout,'(a)') &
1230 "Parameters of the valence-only potentials"
1231 do i=-nthetyp+1,nthetyp-1
1232 write (iout,'(2a)') "Type ",toronelet(i)
1233 do k=0,nbend_kcc_Tb(i)
1234 write(iout,'(i5,f15.5)') k,v1bend_chyb(k,i)
1240 write (2,*) "Start reading THETA_PDB",ithep_pdb
1242 ! write (2,*) 'i=',i
1243 read (ithep_pdb,*,err=111,end=111) &
1244 a0thet(i),(athet(j,i,1,1),j=1,2),&
1245 (bthet(j,i,1,1),j=1,2)
1246 read (ithep_pdb,*,err=111,end=111) (polthet(j,i),j=0,3)
1247 read (ithep_pdb,*,err=111,end=111) (gthet(j,i),j=1,3)
1248 read (ithep_pdb,*,err=111,end=111) theta0(i),sig0(i),sigc0(i)
1249 sigc0(i)=sigc0(i)**2
1252 athet(1,i,1,-1)=athet(1,i,1,1)
1253 athet(2,i,1,-1)=athet(2,i,1,1)
1254 bthet(1,i,1,-1)=-bthet(1,i,1,1)
1255 bthet(2,i,1,-1)=-bthet(2,i,1,1)
1256 athet(1,i,-1,1)=-athet(1,i,1,1)
1257 athet(2,i,-1,1)=-athet(2,i,1,1)
1258 bthet(1,i,-1,1)=bthet(1,i,1,1)
1259 bthet(2,i,-1,1)=bthet(2,i,1,1)
1262 a0thet(i)=a0thet(-i)
1263 athet(1,i,-1,-1)=athet(1,-i,1,1)
1264 athet(2,i,-1,-1)=-athet(2,-i,1,1)
1265 bthet(1,i,-1,-1)=bthet(1,-i,1,1)
1266 bthet(2,i,-1,-1)=-bthet(2,-i,1,1)
1267 athet(1,i,-1,1)=athet(1,-i,1,1)
1268 athet(2,i,-1,1)=-athet(2,-i,1,1)
1269 bthet(1,i,-1,1)=-bthet(1,-i,1,1)
1270 bthet(2,i,-1,1)=bthet(2,-i,1,1)
1271 athet(1,i,1,-1)=-athet(1,-i,1,1)
1272 athet(2,i,1,-1)=athet(2,-i,1,1)
1273 bthet(1,i,1,-1)=bthet(1,-i,1,1)
1274 bthet(2,i,1,-1)=-bthet(2,-i,1,1)
1275 theta0(i)=theta0(-i)
1279 polthet(j,i)=polthet(j,-i)
1282 gthet(j,i)=gthet(j,-i)
1285 write (2,*) "End reading THETA_PDB"
1289 !--------------- Reading theta parameters for nucleic acid-------
1290 read (ithep_nucl,*,err=111,end=111) nthetyp_nucl,ntheterm_nucl,&
1291 ntheterm2_nucl,ntheterm3_nucl,nsingle_nucl,ndouble_nucl
1292 nntheterm_nucl=max0(ntheterm_nucl,ntheterm2_nucl,ntheterm3_nucl)
1293 allocate(ithetyp_nucl(ntyp1_molec(2))) !(-ntyp1:ntyp1)
1294 allocate(aa0thet_nucl(nthetyp_nucl+1,&
1295 nthetyp_nucl+1,nthetyp_nucl+1))
1296 !(-maxthetyp1:maxthetyp1,-maxthetyp1:maxthetyp1,-maxthetyp1:maxthetyp1,2)
1297 allocate(aathet_nucl(ntheterm_nucl+1,nthetyp_nucl+1,&
1298 nthetyp_nucl+1,nthetyp_nucl+1))
1299 !(maxtheterm,-maxthetyp1:maxthetyp1,&
1300 ! -maxthetyp1:maxthetyp1,-maxthetyp1:maxthetyp1,2)
1301 allocate(bbthet_nucl(nsingle_nucl+1,ntheterm2_nucl+1,nthetyp_nucl+1,&
1302 nthetyp_nucl+1,nthetyp_nucl+1))
1303 allocate(ccthet_nucl(nsingle_nucl+1,ntheterm2_nucl+1,nthetyp_nucl+1,&
1304 nthetyp_nucl+1,nthetyp_nucl+1))
1305 allocate(ddthet_nucl(nsingle_nucl+1,ntheterm2_nucl+1,nthetyp_nucl+1,&
1306 nthetyp_nucl+1,nthetyp_nucl+1))
1307 allocate(eethet_nucl(nsingle_nucl+1,ntheterm2_nucl+1,nthetyp_nucl+1,&
1308 nthetyp_nucl+1,nthetyp_nucl+1))
1309 !(maxsingle,maxtheterm2,-maxthetyp1:maxthetyp1,&
1310 ! -maxthetyp1:maxthetyp1,-maxthetyp1:maxthetyp1,2)
1311 allocate(ffthet_nucl(ndouble_nucl+1,ndouble_nucl+1,ntheterm3_nucl+1,&
1312 nthetyp_nucl+1,nthetyp_nucl+1,nthetyp_nucl+1))
1313 allocate(ggthet_nucl(ndouble_nucl+1,ndouble_nucl+1,ntheterm3_nucl+1,&
1314 nthetyp_nucl+1,nthetyp_nucl+1,nthetyp_nucl+1))
1316 !(maxdouble,maxdouble,maxtheterm3,-maxthetyp1:maxthetyp1,&
1317 ! -maxthetyp1:maxthetyp1,-maxthetyp1:maxthetyp1,2))
1319 read (ithep_nucl,*,err=111,end=111) (ithetyp_nucl(i),i=1,ntyp1_molec(2))
1321 aa0thet_nucl(:,:,:)=0.0d0
1322 aathet_nucl(:,:,:,:)=0.0d0
1323 bbthet_nucl(:,:,:,:,:)=0.0d0
1324 ccthet_nucl(:,:,:,:,:)=0.0d0
1325 ddthet_nucl(:,:,:,:,:)=0.0d0
1326 eethet_nucl(:,:,:,:,:)=0.0d0
1327 ffthet_nucl(:,:,:,:,:,:)=0.0d0
1328 ggthet_nucl(:,:,:,:,:,:)=0.0d0
1333 read (ithep_nucl,'(3a)',end=111,err=111) t1,t2,t3
1334 read (ithep_nucl,*,end=111,err=111) aa0thet_nucl(i,j,k)
1335 read (ithep_nucl,*,end=111,err=111)(aathet_nucl(l,i,j,k),l=1,ntheterm_nucl)
1336 read (ithep_nucl,*,end=111,err=111) &
1337 (((bbthet_nucl(lll,ll,i,j,k),lll=1,nsingle_nucl), &
1338 (ccthet_nucl(lll,ll,i,j,k),lll=1,nsingle_nucl), &
1339 (ddthet_nucl(lll,ll,i,j,k),lll=1,nsingle_nucl), &
1340 (eethet_nucl(lll,ll,i,j,k),lll=1,nsingle_nucl)),ll=1,ntheterm2_nucl)
1341 read (ithep_nucl,*,end=111,err=111) &
1342 (((ffthet_nucl(llll,lll,ll,i,j,k),ffthet_nucl(lll,llll,ll,i,j,k), &
1343 ggthet_nucl(llll,lll,ll,i,j,k),ggthet_nucl(lll,llll,ll,i,j,k), &
1344 llll=1,lll-1),lll=2,ndouble_nucl),ll=1,ntheterm3_nucl)
1349 !-------------------------------------------
1350 allocate(nlob(ntyp1)) !(ntyp1)
1351 allocate(bsc(maxlob,ntyp)) !(maxlob,ntyp)
1352 allocate(censc(3,maxlob,-ntyp:ntyp)) !(3,maxlob,-ntyp:ntyp)
1353 allocate(gaussc(3,3,maxlob,-ntyp:ntyp)) !(3,3,maxlob,-ntyp:ntyp)
1360 gaussc(:,:,:,:)=0.0D0
1364 ! Read the parameters of the probability distribution/energy expression
1365 ! of the side chains.
1368 read (irotam,'(3x,i3,f8.3)',end=112,err=112) nlob(i),dsc(i)
1372 dsc_inv(i)=1.0D0/dsc(i)
1383 read(irotam,*,end=112,err=112)(censc(k,1,i),k=1,3),&
1384 ((blower(k,l,1),l=1,k),k=1,3)
1385 censc(1,1,-i)=censc(1,1,i)
1386 censc(2,1,-i)=censc(2,1,i)
1387 censc(3,1,-i)=-censc(3,1,i)
1389 read (irotam,*,end=112,err=112) bsc(j,i)
1390 read (irotam,*,end=112,err=112) (censc(k,j,i),k=1,3),&
1391 ((blower(k,l,j),l=1,k),k=1,3)
1392 censc(1,j,-i)=censc(1,j,i)
1393 censc(2,j,-i)=censc(2,j,i)
1394 censc(3,j,-i)=-censc(3,j,i)
1395 ! BSC is amplitude of Gaussian
1402 akl=akl+blower(k,m,j)*blower(l,m,j)
1406 if (((k.eq.3).and.(l.ne.3)) &
1407 .or.((l.eq.3).and.(k.ne.3))) then
1408 gaussc(k,l,j,-i)=-akl
1409 gaussc(l,k,j,-i)=-akl
1411 gaussc(k,l,j,-i)=akl
1412 gaussc(l,k,j,-i)=akl
1421 write (iout,'(/a)') 'Parameters of side-chain local geometry'
1424 if (nlobi.gt.0) then
1426 write (iout,'(/3a,i2,a,f8.3)') 'Residue type: ',restyp(i,1),&
1427 ' # of gaussian lobes:',nlobi,' dsc:',dsc(i)
1428 write (iout,'(1h&,a,3(2h&&,f8.3,2h&&))') &
1429 'log h',(bsc(j,i),j=1,nlobi)
1430 write (iout,'(1h&,a,3(1h&,f8.3,1h&,f8.3,1h&,f8.3,1h&))') &
1431 'x',((censc(k,j,i),k=1,3),j=1,nlobi)
1433 write (iout,'(2h& ,5(2x,1h&,3(f7.3,1h&)))') &
1434 ((gaussc(k,l,j,i),l=1,3),j=1,nlobi)
1437 write (iout,'(/a,8x,i1,4(25x,i1))') 'Lobe:',(j,j=1,nlobi)
1438 write (iout,'(a,f10.4,4(16x,f10.4))') &
1439 'Center ',(bsc(j,i),j=1,nlobi)
1440 write (iout,'(5(2x,3f8.4))') ((censc(k,j,i),k=1,3),&
1449 ! Read scrot parameters for potentials determined from all-atom AM1 calculations
1450 ! added by Urszula Kozlowska 07/11/2007
1452 !el Maximum number of SC local term fitting function coefficiants
1453 !el integer,parameter :: maxsccoef=65
1455 allocate(sc_parmin(65,ntyp)) !(maxsccoef,ntyp)
1458 read (irotam,*,end=112,err=112)
1460 read (irotam,*,end=112,err=112)
1463 read(irotam,*,end=112,err=112) sc_parmin(j,i)
1467 !---------reading nucleic acid parameters for rotamers-------------------
1468 allocate(sc_parmin_nucl(9,ntyp_molec(2))) !(maxsccoef,ntyp)
1469 do i=1,ntyp_molec(2)
1470 read (irotam_nucl,*,end=112,err=112)
1472 read(irotam_nucl,*,end=112,err=112) sc_parmin_nucl(j,i)
1478 write (iout,*) "Base rotamer parameters"
1479 do i=1,ntyp_molec(2)
1480 write (iout,'(a)') restyp(i,2)
1481 write (iout,'(i5,f10.5)') (i,sc_parmin_nucl(j,i),j=1,9)
1486 ! Read the parameters of the probability distribution/energy expression
1487 ! of the side chains.
1489 write (2,*) "Start reading ROTAM_PDB"
1491 read (irotam_pdb,'(3x,i3,f8.3)',end=112,err=112) nlob(i),dsc(i)
1495 dsc_inv(i)=1.0D0/dsc(i)
1506 read(irotam_pdb,*,end=112,err=112)(censc(k,1,i),k=1,3),&
1507 ((blower(k,l,1),l=1,k),k=1,3)
1509 read (irotam_pdb,*,end=112,err=112) bsc(j,i)
1510 read (irotam_pdb,*,end=112,err=112) (censc(k,j,i),k=1,3),&
1511 ((blower(k,l,j),l=1,k),k=1,3)
1518 akl=akl+blower(k,m,j)*blower(l,m,j)
1528 write (2,*) "End reading ROTAM_PDB"
1534 !C 9/18/99 (AL) Read coefficients of the Fourier expansion of the local
1535 !C interaction energy of the Gly, Ala, and Pro prototypes.
1537 read (ifourier,*) nloctyp
1538 SPLIT_FOURIERTOR = nloctyp.lt.0
1539 nloctyp = iabs(nloctyp)
1540 !C allocate(b1(2,nres)) !(2,-maxtor:maxtor)
1541 !C allocate(b2(2,nres)) !(2,-maxtor:maxtor)
1542 !C allocate(b1tilde(2,nres)) !(2,-maxtor:maxtor)
1543 !C allocate(ctilde(2,2,nres))
1544 !C allocate(dtilde(2,2,nres)) !(2,2,-maxtor:maxtor)
1545 !C allocate(gtb1(2,nres))
1546 !C allocate(gtb2(2,nres))
1547 !C allocate(cc(2,2,nres))
1548 !C allocate(dd(2,2,nres))
1549 !C allocate(ee(2,2,nres))
1550 !C allocate(gtcc(2,2,nres))
1551 !C allocate(gtdd(2,2,nres))
1552 !C allocate(gtee(2,2,nres))
1555 allocate(itype2loc(-ntyp1:ntyp1))
1556 allocate(iloctyp(-nloctyp:nloctyp))
1557 allocate(bnew1(3,2,-nloctyp:nloctyp))
1558 allocate(bnew2(3,2,-nloctyp:nloctyp))
1559 allocate(ccnew(3,2,-nloctyp:nloctyp))
1560 allocate(ddnew(3,2,-nloctyp:nloctyp))
1561 allocate(e0new(3,-nloctyp:nloctyp))
1562 allocate(eenew(2,2,2,-nloctyp:nloctyp))
1563 allocate(bnew1tor(3,2,-nloctyp:nloctyp))
1564 allocate(bnew2tor(3,2,-nloctyp:nloctyp))
1565 allocate(ccnewtor(3,2,-nloctyp:nloctyp))
1566 allocate(ddnewtor(3,2,-nloctyp:nloctyp))
1567 allocate(e0newtor(3,-nloctyp:nloctyp))
1568 allocate(eenewtor(2,2,2,-nloctyp:nloctyp))
1570 read (ifourier,*,end=115,err=115) (itype2loc(i),i=1,ntyp)
1571 read (ifourier,*,end=115,err=115) (iloctyp(i),i=0,nloctyp-1)
1572 itype2loc(ntyp1)=nloctyp
1573 iloctyp(nloctyp)=ntyp1
1575 itype2loc(-i)=-itype2loc(i)
1578 allocate(iloctyp(-nloctyp:nloctyp))
1579 allocate(itype2loc(-ntyp1:ntyp1))
1586 iloctyp(-i)=-iloctyp(i)
1588 !c write (iout,*) "itype2loc",(itype2loc(i),i=1,ntyp1)
1589 !c write (iout,*) "nloctyp",nloctyp,
1590 !c & " iloctyp",(iloctyp(i),i=0,nloctyp)
1591 !c write (iout,*) "itype2loc",(itype2loc(i),i=1,ntyp1)
1592 !c write (iout,*) "nloctyp",nloctyp,
1593 !c & " iloctyp",(iloctyp(i),i=0,nloctyp)
1596 !c write (iout,*) "NEWCORR",i
1597 read (ifourier,*,end=115,err=115)
1600 read (ifourier,*,end=115,err=115) bnew1(ii,j,i)
1603 !c write (iout,*) "NEWCORR BNEW1"
1604 !c write (iout,*) ((bnew1(ii,j,i),ii=1,3),j=1,2)
1607 read (ifourier,*,end=115,err=115) bnew2(ii,j,i)
1610 !c write (iout,*) "NEWCORR BNEW2"
1611 !c write (iout,*) ((bnew2(ii,j,i),ii=1,3),j=1,2)
1613 read (ifourier,*,end=115,err=115) ccnew(kk,1,i)
1614 read (ifourier,*,end=115,err=115) ccnew(kk,2,i)
1616 !c write (iout,*) "NEWCORR CCNEW"
1617 !c write (iout,*) ((ccnew(ii,j,i),ii=1,3),j=1,2)
1619 read (ifourier,*,end=115,err=115) ddnew(kk,1,i)
1620 read (ifourier,*,end=115,err=115) ddnew(kk,2,i)
1622 !c write (iout,*) "NEWCORR DDNEW"
1623 !c write (iout,*) ((ddnew(ii,j,i),ii=1,3),j=1,2)
1627 read (ifourier,*,end=115,err=115) eenew(ii,jj,kk,i)
1631 !c write (iout,*) "NEWCORR EENEW1"
1632 !c write(iout,*)(((eenew(ii,jj,kk,i),kk=1,2),jj=1,2),ii=1,2)
1634 read (ifourier,*,end=115,err=115) e0new(ii,i)
1636 !c write (iout,*) (e0new(ii,i),ii=1,3)
1638 !c write (iout,*) "NEWCORR EENEW"
1641 ccnew(ii,1,i)=ccnew(ii,1,i)/2
1642 ccnew(ii,2,i)=ccnew(ii,2,i)/2
1643 ddnew(ii,1,i)=ddnew(ii,1,i)/2
1644 ddnew(ii,2,i)=ddnew(ii,2,i)/2
1649 bnew1(ii,1,-i)= bnew1(ii,1,i)
1650 bnew1(ii,2,-i)=-bnew1(ii,2,i)
1651 bnew2(ii,1,-i)= bnew2(ii,1,i)
1652 bnew2(ii,2,-i)=-bnew2(ii,2,i)
1655 !c ccnew(ii,1,i)=ccnew(ii,1,i)/2
1656 !c ccnew(ii,2,i)=ccnew(ii,2,i)/2
1657 !c ddnew(ii,1,i)=ddnew(ii,1,i)/2
1658 !c ddnew(ii,2,i)=ddnew(ii,2,i)/2
1659 ccnew(ii,1,-i)=ccnew(ii,1,i)
1660 ccnew(ii,2,-i)=-ccnew(ii,2,i)
1661 ddnew(ii,1,-i)=ddnew(ii,1,i)
1662 ddnew(ii,2,-i)=-ddnew(ii,2,i)
1664 e0new(1,-i)= e0new(1,i)
1665 e0new(2,-i)=-e0new(2,i)
1666 e0new(3,-i)=-e0new(3,i)
1668 eenew(kk,1,1,-i)= eenew(kk,1,1,i)
1669 eenew(kk,1,2,-i)=-eenew(kk,1,2,i)
1670 eenew(kk,2,1,-i)=-eenew(kk,2,1,i)
1671 eenew(kk,2,2,-i)= eenew(kk,2,2,i)
1675 write (iout,'(a)') "Coefficients of the multibody terms"
1676 do i=-nloctyp+1,nloctyp-1
1677 write (iout,*) "Type: ",onelet(iloctyp(i))
1678 write (iout,*) "Coefficients of the expansion of B1"
1680 write (iout,'(3hB1(,i1,1h),3f10.5)') j,(bnew1(k,j,i),k=1,3)
1682 write (iout,*) "Coefficients of the expansion of B2"
1684 write (iout,'(3hB2(,i1,1h),3f10.5)') j,(bnew2(k,j,i),k=1,3)
1686 write (iout,*) "Coefficients of the expansion of C"
1687 write (iout,'(3hC11,3f10.5)') (ccnew(j,1,i),j=1,3)
1688 write (iout,'(3hC12,3f10.5)') (ccnew(j,2,i),j=1,3)
1689 write (iout,*) "Coefficients of the expansion of D"
1690 write (iout,'(3hD11,3f10.5)') (ddnew(j,1,i),j=1,3)
1691 write (iout,'(3hD12,3f10.5)') (ddnew(j,2,i),j=1,3)
1692 write (iout,*) "Coefficients of the expansion of E"
1693 write (iout,'(2hE0,3f10.5)') (e0new(j,i),j=1,3)
1696 write (iout,'(1hE,2i1,2f10.5)') j,k,(eenew(l,j,k,i),l=1,2)
1701 IF (SPLIT_FOURIERTOR) THEN
1703 !c write (iout,*) "NEWCORR TOR",i
1704 read (ifourier,*,end=115,err=115)
1707 read (ifourier,*,end=115,err=115) bnew1tor(ii,j,i)
1710 !c write (iout,*) "NEWCORR BNEW1 TOR"
1711 !c write (iout,*) ((bnew1tor(ii,j,i),ii=1,3),j=1,2)
1714 read (ifourier,*,end=115,err=115) bnew2tor(ii,j,i)
1717 !c write (iout,*) "NEWCORR BNEW2 TOR"
1718 !c write (iout,*) ((bnew2tor(ii,j,i),ii=1,3),j=1,2)
1720 read (ifourier,*,end=115,err=115) ccnewtor(kk,1,i)
1721 read (ifourier,*,end=115,err=115) ccnewtor(kk,2,i)
1723 !c write (iout,*) "NEWCORR CCNEW TOR"
1724 !c write (iout,*) ((ccnew(ii,j,i),ii=1,3),j=1,2)
1726 read (ifourier,*,end=115,err=115) ddnewtor(kk,1,i)
1727 read (ifourier,*,end=115,err=115) ddnewtor(kk,2,i)
1729 !c write (iout,*) "NEWCORR DDNEW TOR"
1730 !c write (iout,*) ((ddnewtor(ii,j,i),ii=1,3),j=1,2)
1734 read (ifourier,*,end=115,err=115) eenewtor(ii,jj,kk,i)
1738 !c write (iout,*) "NEWCORR EENEW1 TOR"
1739 !c write(iout,*)(((eenewtor(ii,jj,kk,i),kk=1,2),jj=1,2),ii=1,2)
1741 read (ifourier,*,end=115,err=115) e0newtor(ii,i)
1743 !c write (iout,*) (e0newtor(ii,i),ii=1,3)
1745 !c write (iout,*) "NEWCORR EENEW TOR"
1748 ccnewtor(ii,1,i)=ccnewtor(ii,1,i)/2
1749 ccnewtor(ii,2,i)=ccnewtor(ii,2,i)/2
1750 ddnewtor(ii,1,i)=ddnewtor(ii,1,i)/2
1751 ddnewtor(ii,2,i)=ddnewtor(ii,2,i)/2
1756 bnew1tor(ii,1,-i)= bnew1tor(ii,1,i)
1757 bnew1tor(ii,2,-i)=-bnew1tor(ii,2,i)
1758 bnew2tor(ii,1,-i)= bnew2tor(ii,1,i)
1759 bnew2tor(ii,2,-i)=-bnew2tor(ii,2,i)
1762 ccnewtor(ii,1,-i)=ccnewtor(ii,1,i)
1763 ccnewtor(ii,2,-i)=-ccnewtor(ii,2,i)
1764 ddnewtor(ii,1,-i)=ddnewtor(ii,1,i)
1765 ddnewtor(ii,2,-i)=-ddnewtor(ii,2,i)
1767 e0newtor(1,-i)= e0newtor(1,i)
1768 e0newtor(2,-i)=-e0newtor(2,i)
1769 e0newtor(3,-i)=-e0newtor(3,i)
1771 eenewtor(kk,1,1,-i)= eenewtor(kk,1,1,i)
1772 eenewtor(kk,1,2,-i)=-eenewtor(kk,1,2,i)
1773 eenewtor(kk,2,1,-i)=-eenewtor(kk,2,1,i)
1774 eenewtor(kk,2,2,-i)= eenewtor(kk,2,2,i)
1778 write (iout,'(a)') &
1779 "Single-body coefficients of the torsional potentials"
1780 do i=-nloctyp+1,nloctyp-1
1781 write (iout,*) "Type: ",onelet(iloctyp(i))
1782 write (iout,*) "Coefficients of the expansion of B1tor"
1784 write (iout,'(3hB1(,i1,1h),3f10.5)') &
1785 j,(bnew1tor(k,j,i),k=1,3)
1787 write (iout,*) "Coefficients of the expansion of B2tor"
1789 write (iout,'(3hB2(,i1,1h),3f10.5)') &
1790 j,(bnew2tor(k,j,i),k=1,3)
1792 write (iout,*) "Coefficients of the expansion of Ctor"
1793 write (iout,'(3hC11,3f10.5)') (ccnewtor(j,1,i),j=1,3)
1794 write (iout,'(3hC12,3f10.5)') (ccnewtor(j,2,i),j=1,3)
1795 write (iout,*) "Coefficients of the expansion of Dtor"
1796 write (iout,'(3hD11,3f10.5)') (ddnewtor(j,1,i),j=1,3)
1797 write (iout,'(3hD12,3f10.5)') (ddnewtor(j,2,i),j=1,3)
1798 write (iout,*) "Coefficients of the expansion of Etor"
1799 write (iout,'(2hE0,3f10.5)') (e0newtor(j,i),j=1,3)
1802 write (iout,'(1hE,2i1,2f10.5)') &
1803 j,k,(eenewtor(l,j,k,i),l=1,2)
1809 do i=-nloctyp+1,nloctyp-1
1812 bnew1tor(ii,j,i)=bnew1(ii,j,i)
1817 bnew2tor(ii,j,i)=bnew2(ii,j,i)
1821 ccnewtor(ii,1,i)=ccnew(ii,1,i)
1822 ccnewtor(ii,2,i)=ccnew(ii,2,i)
1823 ddnewtor(ii,1,i)=ddnew(ii,1,i)
1824 ddnewtor(ii,2,i)=ddnew(ii,2,i)
1827 ENDIF !SPLIT_FOURIER_TOR
1829 allocate(ccold(2,2,-nloctyp-1:nloctyp+1))
1830 allocate(ddold(2,2,-nloctyp-1:nloctyp+1))
1831 allocate(eeold(2,2,-nloctyp-1:nloctyp+1))
1832 allocate(b(13,-nloctyp-1:nloctyp+1))
1834 write (iout,*) "Coefficients of the expansion of Eloc(l1,l2)"
1836 read (ifourier,*,end=115,err=115)
1837 read (ifourier,*,end=115,err=115) (b(ii,i),ii=1,13)
1839 write (iout,*) 'Type ',onelet(iloctyp(i))
1840 write (iout,'(a,i2,a,f10.5)') ('b(',ii,')=',b(ii,i),ii=1,13)
1854 !c B1tilde(1,i) = b(3)
1855 !c! B1tilde(2,i) =-b(5)
1856 !c! B1tilde(1,-i) =-b(3)
1857 !c! B1tilde(2,-i) =b(5)
1858 !c! b1tilde(1,i)=0.0d0
1859 !c b1tilde(2,i)=0.0d0
1864 !cc B1tilde(1,i) = b(3,i)
1865 !cc B1tilde(2,i) =-b(5,i)
1866 !c B1tilde(1,-i) =-b(3,i)
1867 !c B1tilde(2,-i) =b(5,i)
1868 !cc b1tilde(1,i)=0.0d0
1869 !cc b1tilde(2,i)=0.0d0
1870 !cc B2(1,i) = b(2,i)
1871 !cc B2(2,i) = b(4,i)
1873 !c B2(2,-i) =-b(4,i)
1877 CCold(1,1,i)= b(7,i)
1878 CCold(2,2,i)=-b(7,i)
1879 CCold(2,1,i)= b(9,i)
1880 CCold(1,2,i)= b(9,i)
1881 CCold(1,1,-i)= b(7,i)
1882 CCold(2,2,-i)=-b(7,i)
1883 CCold(2,1,-i)=-b(9,i)
1884 CCold(1,2,-i)=-b(9,i)
1889 !c Ctilde(1,1,i)= CCold(1,1,i)
1890 !c Ctilde(1,2,i)= CCold(1,2,i)
1891 !c Ctilde(2,1,i)=-CCold(2,1,i)
1892 !c Ctilde(2,2,i)=-CCold(2,2,i)
1897 !c Ctilde(1,1,i)= CCold(1,1,i)
1898 !c Ctilde(1,2,i)= CCold(1,2,i)
1899 !c Ctilde(2,1,i)=-CCold(2,1,i)
1900 !c Ctilde(2,2,i)=-CCold(2,2,i)
1902 !c Ctilde(1,1,i)=0.0d0
1903 !c Ctilde(1,2,i)=0.0d0
1904 !c Ctilde(2,1,i)=0.0d0
1905 !c Ctilde(2,2,i)=0.0d0
1906 DDold(1,1,i)= b(6,i)
1907 DDold(2,2,i)=-b(6,i)
1908 DDold(2,1,i)= b(8,i)
1909 DDold(1,2,i)= b(8,i)
1910 DDold(1,1,-i)= b(6,i)
1911 DDold(2,2,-i)=-b(6,i)
1912 DDold(2,1,-i)=-b(8,i)
1913 DDold(1,2,-i)=-b(8,i)
1918 !c Dtilde(1,1,i)= DD(1,1,i)
1919 !c Dtilde(1,2,i)= DD(1,2,i)
1920 !c Dtilde(2,1,i)=-DD(2,1,i)
1921 !c Dtilde(2,2,i)=-DD(2,2,i)
1923 !c Dtilde(1,1,i)=0.0d0
1924 !c Dtilde(1,2,i)=0.0d0
1925 !c Dtilde(2,1,i)=0.0d0
1926 !c Dtilde(2,2,i)=0.0d0
1927 EEold(1,1,i)= b(10,i)+b(11,i)
1928 EEold(2,2,i)=-b(10,i)+b(11,i)
1929 EEold(2,1,i)= b(12,i)-b(13,i)
1930 EEold(1,2,i)= b(12,i)+b(13,i)
1931 EEold(1,1,-i)= b(10,i)+b(11,i)
1932 EEold(2,2,-i)=-b(10,i)+b(11,i)
1933 EEold(2,1,-i)=-b(12,i)+b(13,i)
1934 EEold(1,2,-i)=-b(12,i)-b(13,i)
1935 write(iout,*) "TU DOCHODZE"
1941 !c ee(2,1,i)=ee(1,2,i)
1946 "Coefficients of the cumulants (independent of valence angles)"
1947 do i=-nloctyp+1,nloctyp-1
1948 write (iout,*) 'Type ',onelet(iloctyp(i))
1950 write(iout,'(2f10.5)') B(3,i),B(5,i)
1952 write(iout,'(2f10.5)') B(2,i),B(4,i)
1955 write (iout,'(2f10.5)') CCold(j,1,i),CCold(j,2,i)
1959 write (iout,'(2f10.5)') DDold(j,1,i),DDold(j,2,i)
1963 write (iout,'(2f10.5)') EEold(j,1,i),EEold(j,2,i)
1972 ! Read torsional parameters in old format
1974 allocate(itortyp(ntyp1)) !(-ntyp1:ntyp1)
1976 read (itorp,*,end=113,err=113) ntortyp,nterm_old
1977 if (lprint)write (iout,*) 'ntortyp,nterm',ntortyp,nterm_old
1978 read (itorp,*,end=113,err=113) (itortyp(i),i=1,ntyp)
1980 !el from energy module--------
1981 allocate(v1(nterm_old,ntortyp,ntortyp))
1982 allocate(v2(nterm_old,ntortyp,ntortyp)) !(maxterm,-maxtor:maxtor,-maxtor:maxtor)
1983 !el---------------------------
1988 read (itorp,*,end=113,err=113) kk,v1(k,j,i),v2(k,j,i)
1994 write (iout,'(/a/)') 'Torsional constants:'
1997 write (iout,'(2i3,6f10.5)') i,j,(v1(k,i,j),k=1,nterm_old)
1998 write (iout,'(6x,6f10.5)') (v2(k,i,j),k=1,nterm_old)
2004 ! Read torsional parameters
2006 IF (TOR_MODE.eq.0) THEN
2007 allocate(itortyp(-ntyp1:ntyp1)) !(-ntyp1:ntyp1)
2008 read (itorp,*,end=113,err=113) ntortyp
2009 !el from energy module---------
2010 allocate(nterm(-ntortyp:ntortyp,-ntortyp:ntortyp,2)) !(-maxtor:maxtor,-maxtor:maxtor,2)
2011 allocate(nlor(-ntortyp:ntortyp,-ntortyp:ntortyp,2)) !(-maxtor:maxtor,-maxtor:maxtor,2)
2013 allocate(vlor1(maxlor,-ntortyp:ntortyp,-ntortyp:ntortyp)) !(maxlor,-maxtor:maxtor,-maxtor:maxtor)
2014 allocate(vlor2(maxlor,ntortyp,ntortyp))
2015 allocate(vlor3(maxlor,ntortyp,ntortyp)) !(maxlor,maxtor,maxtor)
2016 allocate(v0(-ntortyp:ntortyp,-ntortyp:ntortyp,2)) !(-maxtor:maxtor,-maxtor:maxtor,2)
2018 allocate(v1(maxterm,-ntortyp:ntortyp,-ntortyp:ntortyp,2))
2019 allocate(v2(maxterm,-ntortyp:ntortyp,-ntortyp:ntortyp,2)) !(maxterm,-maxtor:maxtor,-maxtor:maxtor,2)
2020 !el---------------------------
2023 !el---------------------------
2025 read (itorp,*,end=113,err=113) (itortyp(i),i=1,ntyp)
2027 itortyp(i)=-itortyp(-i)
2029 itortyp(ntyp1)=ntortyp
2030 itortyp(-ntyp1)=-ntortyp
2032 write (iout,*) 'ntortyp',ntortyp
2034 do j=-ntortyp+1,ntortyp-1
2035 read (itorp,*,end=113,err=113) nterm(i,j,iblock),&
2037 nterm(-i,-j,iblock)=nterm(i,j,iblock)
2038 nlor(-i,-j,iblock)=nlor(i,j,iblock)
2041 do k=1,nterm(i,j,iblock)
2042 read (itorp,*,end=113,err=113) kk,v1(k,i,j,iblock),&
2044 v1(k,-i,-j,iblock)=v1(k,i,j,iblock)
2045 v2(k,-i,-j,iblock)=-v2(k,i,j,iblock)
2046 v0ij=v0ij+si*v1(k,i,j,iblock)
2048 ! write(iout,*) i,j,k,iblock,nterm(i,j,iblock) !
2049 ! write(iout,*) v1(k,-i,-j,iblock),v1(k,i,j,iblock),&!
2050 ! v2(k,-i,-j,iblock),v2(k,i,j,iblock)!
2052 do k=1,nlor(i,j,iblock)
2053 read (itorp,*,end=113,err=113) kk,vlor1(k,i,j),&
2054 vlor2(k,i,j),vlor3(k,i,j)
2055 v0ij=v0ij+vlor1(k,i,j)/(1+vlor3(k,i,j)**2)
2058 v0(-i,-j,iblock)=v0ij
2064 write (iout,'(/a/)') 'Torsional constants:'
2066 do i=-ntortyp,ntortyp
2067 do j=-ntortyp,ntortyp
2068 write (iout,*) 'ityp',i,' jtyp',j
2069 write (iout,*) 'Fourier constants'
2070 do k=1,nterm(i,j,iblock)
2071 write (iout,'(2(1pe15.5))') v1(k,i,j,iblock),&
2074 write (iout,*) 'Lorenz constants'
2075 do k=1,nlor(i,j,iblock)
2076 write (iout,'(3(1pe15.5))') &
2077 vlor1(k,i,j),vlor2(k,i,j),vlor3(k,i,j)
2083 !elwrite (iout,'(/a/)') 'Torsional constants:',vlor1(k,i,j),vlor2(k,i,j),vlor3(k,i,j)
2085 ! 6/23/01 Read parameters for double torsionals
2087 !el from energy module------------
2088 allocate(v1c(2,maxtermd_1,-ntortyp+1:ntortyp-1,-ntortyp+1:ntortyp-1,-ntortyp+1:ntortyp-1,2))
2089 allocate(v1s(2,maxtermd_1,-ntortyp+1:ntortyp-1,-ntortyp+1:ntortyp-1,-ntortyp+1:ntortyp-1,2))
2090 !(2,maxtermd_1,-maxtor:maxtor,-maxtor:maxtor,-maxtor:maxtor,2)
2091 allocate(v2c(maxtermd_2,maxtermd_2,-ntortyp+1:ntortyp-1,-ntortyp+1:ntortyp-1,-ntortyp+1:ntortyp-1,2))
2092 allocate(v2s(maxtermd_2,maxtermd_2,-ntortyp+1:ntortyp-1,-ntortyp+1:ntortyp-1,-ntortyp+1:ntortyp-1,2))
2093 !(maxtermd_2,maxtermd_2,-maxtor:maxtor,-maxtor:maxtor,-maxtor:maxtor,2)
2094 allocate(ntermd_1(-ntortyp+1:ntortyp-1,-ntortyp+1:ntortyp-1,-ntortyp+1:ntortyp-1,2))
2095 allocate(ntermd_2(-ntortyp+1:ntortyp-1,-ntortyp+1:ntortyp-1,-ntortyp+1:ntortyp-1,2))
2096 !(-maxtor:maxtor,-maxtor:maxtor,-maxtor:maxtor,2)
2097 !---------------------------------
2101 do j=-ntortyp+1,ntortyp-1
2102 do k=-ntortyp+1,ntortyp-1
2103 read (itordp,'(3a1)',end=114,err=114) t1,t2,t3
2104 ! write (iout,*) "OK onelett",
2107 if (t1.ne.toronelet(i) .or. t2.ne.toronelet(j) &
2108 .or. t3.ne.toronelet(k)) then
2109 write (iout,*) "Error in double torsional parameter file",&
2112 call MPI_Finalize(Ierror)
2114 stop "Error in double torsional parameter file"
2116 read (itordp,*,end=114,err=114) ntermd_1(i,j,k,iblock),&
2117 ntermd_2(i,j,k,iblock)
2118 ntermd_1(-i,-j,-k,iblock)=ntermd_1(i,j,k,iblock)
2119 ntermd_2(-i,-j,-k,iblock)=ntermd_2(i,j,k,iblock)
2120 read (itordp,*,end=114,err=114) (v1c(1,l,i,j,k,iblock),l=1,&
2121 ntermd_1(i,j,k,iblock))
2122 read (itordp,*,end=114,err=114) (v1s(1,l,i,j,k,iblock),l=1,&
2123 ntermd_1(i,j,k,iblock))
2124 read (itordp,*,end=114,err=114) (v1c(2,l,i,j,k,iblock),l=1,&
2125 ntermd_1(i,j,k,iblock))
2126 read (itordp,*,end=114,err=114) (v1s(2,l,i,j,k,iblock),l=1,&
2127 ntermd_1(i,j,k,iblock))
2128 ! Martix of D parameters for one dimesional foureir series
2129 do l=1,ntermd_1(i,j,k,iblock)
2130 v1c(1,l,-i,-j,-k,iblock)=v1c(1,l,i,j,k,iblock)
2131 v1s(1,l,-i,-j,-k,iblock)=-v1s(1,l,i,j,k,iblock)
2132 v1c(2,l,-i,-j,-k,iblock)=v1c(2,l,i,j,k,iblock)
2133 v1s(2,l,-i,-j,-k,iblock)=-v1s(2,l,i,j,k,iblock)
2134 ! write(iout,*) "whcodze" ,
2135 ! & v1s(2,l,-i,-j,-k,iblock),v1s(2,l,i,j,k,iblock)
2137 read (itordp,*,end=114,err=114) ((v2c(l,m,i,j,k,iblock),&
2138 v2c(m,l,i,j,k,iblock),v2s(l,m,i,j,k,iblock),&
2139 v2s(m,l,i,j,k,iblock),&
2140 m=1,l-1),l=1,ntermd_2(i,j,k,iblock))
2141 ! Martix of D parameters for two dimesional fourier series
2142 do l=1,ntermd_2(i,j,k,iblock)
2144 v2c(l,m,-i,-j,-k,iblock)=v2c(l,m,i,j,k,iblock)
2145 v2c(m,l,-i,-j,-k,iblock)=v2c(m,l,i,j,k,iblock)
2146 v2s(l,m,-i,-j,-k,iblock)=-v2s(l,m,i,j,k,iblock)
2147 v2s(m,l,-i,-j,-k,iblock)=-v2s(m,l,i,j,k,iblock)
2156 write (iout,*) 'Constants for double torsionals'
2159 do j=-ntortyp+1,ntortyp-1
2160 do k=-ntortyp+1,ntortyp-1
2161 write (iout,*) 'ityp',i,' jtyp',j,' ktyp',k,&
2162 ' nsingle',ntermd_1(i,j,k,iblock),&
2163 ' ndouble',ntermd_2(i,j,k,iblock)
2165 write (iout,*) 'Single angles:'
2166 do l=1,ntermd_1(i,j,k,iblock)
2167 write (iout,'(i5,2f10.5,5x,2f10.5,5x,2f10.5)') l,&
2168 v1c(1,l,i,j,k,iblock),v1s(1,l,i,j,k,iblock),&
2169 v1c(2,l,i,j,k,iblock),v1s(2,l,i,j,k,iblock),&
2170 v1s(1,l,-i,-j,-k,iblock),v1s(2,l,-i,-j,-k,iblock)
2173 write (iout,*) 'Pairs of angles:'
2174 write (iout,'(3x,20i10)') (l,l=1,ntermd_2(i,j,k,iblock))
2175 do l=1,ntermd_2(i,j,k,iblock)
2176 write (iout,'(i5,20f10.5)') &
2177 l,(v2c(l,m,i,j,k,iblock),m=1,ntermd_2(i,j,k,iblock))
2180 write (iout,'(3x,20i10)') (l,l=1,ntermd_2(i,j,k,iblock))
2181 do l=1,ntermd_2(i,j,k,iblock)
2182 write (iout,'(i5,20f10.5)') &
2183 l,(v2s(l,m,i,j,k,iblock),m=1,ntermd_2(i,j,k,iblock)),&
2184 (v2s(l,m,-i,-j,-k,iblock),m=1,ntermd_2(i,j,k,iblock))
2194 itype2loc(i)=itortyp(i)
2198 ELSE IF (TOR_MODE.eq.1) THEN
2200 !C read valence-torsional parameters
2201 read (itorp,*,end=121,err=121) ntortyp
2203 write (iout,*) "Valence-torsional parameters read in ntortyp",&
2205 read (itorp,*,end=121,err=121) (itortyp(i),i=1,ntyp)
2206 write (iout,*) "itortyp_kcc",(itortyp(i),i=1,ntyp)
2209 itype2loc(i)=itortyp(i)
2213 itortyp(i)=-itortyp(-i)
2215 do i=-ntortyp+1,ntortyp-1
2216 do j=-ntortyp+1,ntortyp-1
2217 !C first we read the cos and sin gamma parameters
2218 read (itorp,'(13x,a)',end=121,err=121) string
2219 write (iout,*) i,j,string
2220 read (itorp,*,end=121,err=121) &
2221 nterm_kcc(j,i),nterm_kcc_Tb(j,i)
2222 !C read (itorkcc,*,end=121,err=121) nterm_kcc_Tb(j,i)
2223 do k=1,nterm_kcc(j,i)
2224 do l=1,nterm_kcc_Tb(j,i)
2225 do ll=1,nterm_kcc_Tb(j,i)
2226 read (itorp,*,end=121,err=121) ii,jj,kk, &
2227 v1_kcc(ll,l,k,j,i),v2_kcc(ll,l,k,j,i)
2235 !c AL 4/8/16: Calculate coefficients from one-body parameters
2237 allocate(itortyp(-ntyp1:ntyp1)) !(-ntyp1:ntyp1)
2238 allocate(nterm_kcc(-ntyp1:ntyp1,-ntyp1:ntyp1))
2239 allocate(nterm_kcc_Tb(-ntyp1:ntyp1,-ntyp1:ntyp1))
2240 allocate(v1_kcc(6,6,6,-ntyp1:ntyp1,-ntyp1:ntyp1))
2241 allocate(v2_kcc(6,6,6,-ntyp1:ntyp1,-ntyp1:ntyp1))
2244 print *,i,itortyp(i)
2245 itortyp(i)=itype2loc(i)
2248 "Val-tor parameters calculated from cumulant coefficients ntortyp"&
2250 do i=-ntortyp+1,ntortyp-1
2251 do j=-ntortyp+1,ntortyp-1
2254 do k=1,nterm_kcc_Tb(j,i)
2255 do l=1,nterm_kcc_Tb(j,i)
2256 v1_kcc(k,l,1,i,j)=bnew1tor(k,1,i)*bnew2tor(l,1,j)&
2257 +bnew1tor(k,2,i)*bnew2tor(l,2,j)
2258 v2_kcc(k,l,1,i,j)=bnew1tor(k,1,i)*bnew2tor(l,2,j)&
2259 +bnew1tor(k,2,i)*bnew2tor(l,1,j)
2262 do k=1,nterm_kcc_Tb(j,i)
2263 do l=1,nterm_kcc_Tb(j,i)
2265 v1_kcc(k,l,2,i,j)=-(ccnewtor(k,1,i)*ddnewtor(l,1,j) &
2266 -ccnewtor(k,2,i)*ddnewtor(l,2,j))
2267 v2_kcc(k,l,2,i,j)=-(ccnewtor(k,2,i)*ddnewtor(l,1,j) &
2268 +ccnewtor(k,1,i)*ddnewtor(l,2,j))
2270 v1_kcc(k,l,2,i,j)=-0.25*(ccnewtor(k,1,i)*ddnewtor(l,1,j) &
2271 -ccnewtor(k,2,i)*ddnewtor(l,2,j))
2272 v2_kcc(k,l,2,i,j)=-0.25*(ccnewtor(k,2,i)*ddnewtor(l,1,j) &
2273 +ccnewtor(k,1,i)*ddnewtor(l,2,j))
2277 !c f(theta,gamma)=-(b21(theta)*b11(theta)+b12(theta)*b22(theta))*cos(gamma)-(b22(theta)*b11(theta)+b21(theta)*b12(theta))*sin(gamma)+(c11(theta)*d11(theta)-c12(theta)*d12(theta))*cos(2*gamma)+(c12(theta)*d11(theta)+c11(theta)*d12(theta))*sin(2*gamma)
2281 write (iout,*) "TOR_MODE>1 only with NEWCORR"
2286 if (tor_mode.gt.0 .and. lprint) then
2287 !c Print valence-torsional parameters
2288 write (iout,'(a)') &
2289 "Parameters of the valence-torsional potentials"
2290 do i=-ntortyp+1,ntortyp-1
2291 do j=-ntortyp+1,ntortyp-1
2292 write (iout,'(3a)') "Type ",toronelet(i),toronelet(j)
2293 write (iout,'(3a5,2a15)') "itor","ival","jval","v_kcc","v2_kcc"
2294 do k=1,nterm_kcc(j,i)
2295 do l=1,nterm_kcc_Tb(j,i)
2296 do ll=1,nterm_kcc_Tb(j,i)
2297 write (iout,'(3i5,2f15.4)')&
2298 k,l-1,ll-1,v1_kcc(ll,l,k,j,i),v2_kcc(ll,l,k,j,i)
2306 allocate(itortyp_nucl(ntyp1_molec(2))) !(-ntyp1:ntyp1)
2307 read (itorp_nucl,*,end=113,err=113) ntortyp_nucl
2308 ! print *,"ntortyp_nucl",ntortyp_nucl,ntyp_molec(2)
2309 !el from energy module---------
2310 allocate(nterm_nucl(ntortyp_nucl,ntortyp_nucl)) !(-maxtor:maxtor,-maxtor:maxtor,2)
2311 allocate(nlor_nucl(ntortyp_nucl,ntortyp_nucl)) !(-maxtor:maxtor,-maxtor:maxtor,2)
2313 allocate(vlor1_nucl(maxlor,ntortyp_nucl,ntortyp_nucl)) !(maxlor,-maxtor:maxtor,-maxtor:maxtor)
2314 allocate(vlor2_nucl(maxlor,ntortyp_nucl,ntortyp_nucl))
2315 allocate(vlor3_nucl(maxlor,ntortyp_nucl,ntortyp_nucl)) !(maxlor,maxtor,maxtor)
2316 allocate(v0_nucl(ntortyp_nucl,ntortyp_nucl)) !(-maxtor:maxtor,-maxtor:maxtor,2)
2318 allocate(v1_nucl(maxterm,ntortyp_nucl,ntortyp_nucl))
2319 allocate(v2_nucl(maxterm,ntortyp_nucl,ntortyp_nucl)) !(maxterm,-maxtor:maxtor,-maxtor:maxtor,2)
2320 !el---------------------------
2323 !el--------------------
2324 read (itorp_nucl,*,end=113,err=113) &
2325 (itortyp_nucl(i),i=1,ntyp_molec(2))
2326 ! print *,itortyp_nucl(:)
2327 !c write (iout,*) 'ntortyp',ntortyp
2330 read (itorp_nucl,*,end=113,err=113) nterm_nucl(i,j),nlor_nucl(i,j)
2331 ! print *,nterm_nucl(i,j),nlor_nucl(i,j)
2334 do k=1,nterm_nucl(i,j)
2335 read (itorp_nucl,*,end=113,err=113) kk,v1_nucl(k,i,j),v2_nucl(k,i,j)
2336 v0ij=v0ij+si*v1_nucl(k,i,j)
2339 do k=1,nlor_nucl(i,j)
2340 read (itorp,*,end=113,err=113) kk,vlor1_nucl(k,i,j),&
2341 vlor2_nucl(k,i,j),vlor3_nucl(k,i,j)
2342 v0ij=v0ij+vlor1_nucl(k,i,j)/(1+vlor3_nucl(k,i,j)**2)
2348 ! Read of Side-chain backbone correlation parameters
2349 ! Modified 11 May 2012 by Adasko
2352 read (isccor,*,end=119,err=119) nsccortyp
2354 !el from module energy-------------
2355 allocate(nlor_sccor(nsccortyp,nsccortyp)) !(-ntyp:ntyp,-ntyp:ntyp)
2356 allocate(vlor1sccor(maxterm_sccor,nsccortyp,nsccortyp))
2357 allocate(vlor2sccor(maxterm_sccor,nsccortyp,nsccortyp))
2358 allocate(vlor3sccor(maxterm_sccor,nsccortyp,nsccortyp)) !(maxterm_sccor,20,20)
2359 !-----------------------------------
2361 !el from module energy-------------
2362 allocate(isccortyp(-ntyp:ntyp)) !(-ntyp:ntyp)
2364 read (isccor,*,end=119,err=119) (isccortyp(i),i=1,ntyp)
2366 isccortyp(i)=-isccortyp(-i)
2368 iscprol=isccortyp(20)
2369 ! write (iout,*) 'ntortyp',ntortyp
2371 !c maxinter is maximum interaction sites
2372 !el from module energy---------
2373 allocate(nterm_sccor(-nsccortyp:nsccortyp,-nsccortyp:nsccortyp)) !(-ntyp:ntyp,-ntyp:ntyp)
2374 allocate(v1sccor(maxterm_sccor,maxinter,-nsccortyp:nsccortyp,&
2375 -nsccortyp:nsccortyp))
2376 allocate(v2sccor(maxterm_sccor,maxinter,-nsccortyp:nsccortyp,&
2377 -nsccortyp:nsccortyp)) !(maxterm_sccor,3,-ntyp:ntyp,-ntyp:ntyp)
2378 allocate(v0sccor(maxinter,-nsccortyp:nsccortyp,&
2379 -nsccortyp:nsccortyp)) !(maxterm_sccor,-ntyp:ntyp,-ntyp:ntyp)
2380 !-----------------------------------
2384 read (isccor,*,end=119,err=119) &
2385 nterm_sccor(i,j),nlor_sccor(i,j)
2391 nterm_sccor(-i,j)=nterm_sccor(i,j)
2392 nterm_sccor(-i,-j)=nterm_sccor(i,j)
2393 nterm_sccor(i,-j)=nterm_sccor(i,j)
2394 do k=1,nterm_sccor(i,j)
2395 read (isccor,*,end=119,err=119) kk,v1sccor(k,l,i,j),&
2397 if (j.eq.iscprol) then
2398 if (i.eq.isccortyp(10)) then
2399 v1sccor(k,l,i,-j)=v1sccor(k,l,i,j)
2400 v2sccor(k,l,i,-j)=-v2sccor(k,l,i,j)
2402 v1sccor(k,l,i,-j)=v1sccor(k,l,i,j)*0.5d0 &
2403 +v2sccor(k,l,i,j)*dsqrt(0.75d0)
2404 v2sccor(k,l,i,-j)=-v2sccor(k,l,i,j)*0.5d0 &
2405 +v1sccor(k,l,i,j)*dsqrt(0.75d0)
2406 v1sccor(k,l,-i,-j)=v1sccor(k,l,i,j)
2407 v2sccor(k,l,-i,-j)=-v2sccor(k,l,i,j)
2408 v1sccor(k,l,-i,j)=v1sccor(k,l,i,-j)
2409 v2sccor(k,l,-i,j)=-v2sccor(k,l,i,-j)
2412 if (i.eq.isccortyp(10)) then
2413 v1sccor(k,l,i,-j)=v1sccor(k,l,i,j)
2414 v2sccor(k,l,i,-j)=-v2sccor(k,l,i,j)
2416 if (j.eq.isccortyp(10)) then
2417 v1sccor(k,l,-i,j)=v1sccor(k,l,i,j)
2418 v2sccor(k,l,-i,j)=-v2sccor(k,l,i,j)
2420 v1sccor(k,l,i,-j)=-v1sccor(k,l,i,j)
2421 v2sccor(k,l,i,-j)=-v2sccor(k,l,i,j)
2422 v1sccor(k,l,-i,-j)=v1sccor(k,l,i,j)
2423 v2sccor(k,l,-i,-j)=-v2sccor(k,l,i,j)
2424 v1sccor(k,l,-i,j)=v1sccor(k,l,i,-j)
2425 v2sccor(k,l,-i,j)=-v2sccor(k,l,i,-j)
2429 v0ijsccor=v0ijsccor+si*v1sccor(k,l,i,j)
2430 v0ijsccor1=v0ijsccor+si*v1sccor(k,l,-i,j)
2431 v0ijsccor2=v0ijsccor+si*v1sccor(k,l,i,-j)
2432 v0ijsccor3=v0ijsccor+si*v1sccor(k,l,-i,-j)
2435 do k=1,nlor_sccor(i,j)
2436 read (isccor,*,end=119,err=119) kk,vlor1sccor(k,i,j),&
2437 vlor2sccor(k,i,j),vlor3sccor(k,i,j)
2438 v0ijsccor=v0ijsccor+vlor1sccor(k,i,j)/ &
2439 (1+vlor3sccor(k,i,j)**2)
2441 v0sccor(l,i,j)=v0ijsccor
2442 v0sccor(l,-i,j)=v0ijsccor1
2443 v0sccor(l,i,-j)=v0ijsccor2
2444 v0sccor(l,-i,-j)=v0ijsccor3
2450 !el from module energy-------------
2451 allocate(isccortyp(ntyp)) !(-ntyp:ntyp)
2453 read (isccor,*,end=119,err=119) (isccortyp(i),i=1,ntyp)
2454 ! write (iout,*) 'ntortyp',ntortyp
2456 !c maxinter is maximum interaction sites
2457 !el from module energy---------
2458 allocate(nterm_sccor(nsccortyp,nsccortyp)) !(-ntyp:ntyp,-ntyp:ntyp)
2459 allocate(v1sccor(maxterm_sccor,maxinter,nsccortyp,nsccortyp))
2460 allocate(v2sccor(maxterm_sccor,maxinter,nsccortyp,nsccortyp)) !(maxterm_sccor,3,-ntyp:ntyp,-ntyp:ntyp)
2461 allocate(v0sccor(maxinter,nsccortyp,nsccortyp)) !???(maxterm_sccor,-ntyp:ntyp,-ntyp:ntyp)
2462 !-----------------------------------
2466 read (isccor,*,end=119,err=119) &
2467 nterm_sccor(i,j),nlor_sccor(i,j)
2471 do k=1,nterm_sccor(i,j)
2472 read (isccor,*,end=119,err=119) kk,v1sccor(k,l,i,j),&
2474 v0ijsccor=v0ijsccor+si*v1sccor(k,l,i,j)
2477 do k=1,nlor_sccor(i,j)
2478 read (isccor,*,end=119,err=119) kk,vlor1sccor(k,i,j),&
2479 vlor2sccor(k,i,j),vlor3sccor(k,i,j)
2480 v0ijsccor=v0ijsccor+vlor1sccor(k,i,j)/ &
2481 (1+vlor3sccor(k,i,j)**2)
2483 v0sccor(l,i,j)=v0ijsccor !el ,iblock
2492 write (iout,'(/a/)') 'Torsional constants:'
2495 write (iout,*) 'ityp',i,' jtyp',j
2496 write (iout,*) 'Fourier constants'
2497 do k=1,nterm_sccor(i,j)
2498 write (iout,'(2(1pe15.5))') v1sccor(k,l,i,j),v2sccor(k,l,i,j)
2500 write (iout,*) 'Lorenz constants'
2501 do k=1,nlor_sccor(i,j)
2502 write (iout,'(3(1pe15.5))') &
2503 vlor1sccor(k,i,j),vlor2sccor(k,i,j),vlor3sccor(k,i,j)
2510 ! 9/18/99 (AL) Read coefficients of the Fourier expansion of the local
2511 ! interaction energy of the Gly, Ala, and Pro prototypes.
2514 ! Read electrostatic-interaction parameters
2519 write (iout,'(/a)') 'Electrostatic interaction constants:'
2520 write (iout,'(1x,a,1x,a,10x,a,11x,a,11x,a,11x,a)') &
2521 'IT','JT','APP','BPP','AEL6','AEL3'
2523 read (ielep,*,end=116,err=116) ((epp(i,j),j=1,2),i=1,2)
2524 read (ielep,*,end=116,err=116) ((rpp(i,j),j=1,2),i=1,2)
2525 read (ielep,*,end=116,err=116) ((elpp6(i,j),j=1,2),i=1,2)
2526 read (ielep,*,end=116,err=116) ((elpp3(i,j),j=1,2),i=1,2)
2531 app (i,j)=epp(i,j)*rri*rri
2532 bpp (i,j)=-2.0D0*epp(i,j)*rri
2533 ael6(i,j)=elpp6(i,j)*4.2D0**6
2534 ael3(i,j)=elpp3(i,j)*4.2D0**3
2536 if (lprint) write(iout,'(2i3,4(1pe15.4))')i,j,app(i,j),bpp(i,j),&
2542 ! Read side-chain interaction parameters.
2544 !el from module energy - COMMON.INTERACT-------
2545 allocate(eps(ntyp,ntyp),sigmaii(ntyp,ntyp),rs0(ntyp,ntyp)) !(ntyp,ntyp)
2546 allocate(augm(ntyp,ntyp)) !(ntyp,ntyp)
2547 allocate(eps_scp(ntyp,2),rscp(ntyp,2)) !(ntyp,2)
2549 allocate(sigma0(ntyp),rr0(ntyp),sigii(ntyp)) !(ntyp)
2550 allocate(chip(ntyp1),alp(ntyp1)) !(ntyp)
2551 allocate(epslip(ntyp,ntyp))
2559 !--------------------------------
2561 read (isidep,*,end=117,err=117) ipot,expon
2562 if (ipot.lt.1 .or. ipot.gt.5) then
2563 write (iout,'(2a)') 'Error while reading SC interaction',&
2564 'potential file - unknown potential type.'
2566 call MPI_Finalize(Ierror)
2572 write(iout,'(/3a,2i3)') 'Potential is ',potname(ipot),&
2573 ', exponents are ',expon,2*expon
2574 ! goto (10,20,30,30,40) ipot
2576 !----------------------- LJ potential ---------------------------------
2578 ! 10 read (isidep,*,end=117,err=117)((eps(i,j),j=i,ntyp),i=1,ntyp),&
2579 read (isidep,*,end=117,err=117)((eps(i,j),j=i,ntyp),i=1,ntyp),&
2580 (sigma0(i),i=1,ntyp)
2582 write (iout,'(/a/)') 'Parameters of the LJ potential:'
2583 write (iout,'(a/)') 'The epsilon array:'
2584 call printmat(ntyp,ntyp,ntyp,iout,restyp,eps)
2585 write (iout,'(/a)') 'One-body parameters:'
2586 write (iout,'(a,4x,a)') 'residue','sigma'
2587 write (iout,'(a3,6x,f10.5)') (restyp(i,1),sigma0(i),i=1,ntyp)
2590 !----------------------- LJK potential --------------------------------
2592 ! 20 read (isidep,*,end=117,err=117)((eps(i,j),j=i,ntyp),i=1,ntyp),&
2593 read (isidep,*,end=117,err=117)((eps(i,j),j=i,ntyp),i=1,ntyp),&
2594 (sigma0(i),i=1,ntyp),(rr0(i),i=1,ntyp)
2596 write (iout,'(/a/)') 'Parameters of the LJK potential:'
2597 write (iout,'(a/)') 'The epsilon array:'
2598 call printmat(ntyp,ntyp,ntyp,iout,restyp,eps)
2599 write (iout,'(/a)') 'One-body parameters:'
2600 write (iout,'(a,4x,2a)') 'residue',' sigma ',' r0 '
2601 write (iout,'(a3,6x,2f10.5)') (restyp(i,1),sigma0(i),rr0(i),&
2605 !---------------------- GB or BP potential -----------------------------
2608 ! print *,"I AM in SCELE",scelemode
2609 if (scelemode.eq.0) then
2611 read (isidep,*,end=117,err=117)(eps(i,j),j=i,ntyp)
2613 read (isidep,*,end=117,err=117)(sigma0(i),i=1,ntyp)
2614 read (isidep,*,end=117,err=117)(sigii(i),i=1,ntyp)
2615 read (isidep,*,end=117,err=117)(chip(i),i=1,ntyp)
2616 read (isidep,*,end=117,err=117)(alp(i),i=1,ntyp)
2618 read (isidep,*,end=117,err=117)(epslip(i,j),j=i,ntyp)
2621 ! For the GB potential convert sigma'**2 into chi'
2624 chip(i)=(chip(i)-1.0D0)/(chip(i)+1.0D0)
2628 write (iout,'(/a/)') 'Parameters of the BP potential:'
2629 write (iout,'(a/)') 'The epsilon array:'
2630 call printmat(ntyp,ntyp,ntyp,iout,restyp,eps)
2631 write (iout,'(/a)') 'One-body parameters:'
2632 write (iout,'(a,4x,4a)') 'residue',' sigma ','s||/s_|_^2',&
2634 write (iout,'(a3,6x,4f10.5)') (restyp(i,1),sigma0(i),sigii(i),&
2635 chip(i),alp(i),i=1,ntyp)
2638 ! print *,ntyp,"NTYP"
2639 allocate(icharge(ntyp1))
2640 ! print *,ntyp,icharge(i)
2642 read (isidep,*) (icharge(i),i=1,ntyp)
2643 print *,ntyp,icharge(i)
2644 ! if(.not.allocated(eps)) allocate(eps(-ntyp
2645 !c write (2,*) "icharge",(icharge(i),i=1,ntyp)
2646 allocate(alphapol(ntyp,ntyp),epshead(ntyp,ntyp),sig0head(ntyp,ntyp))
2647 allocate(sigiso1(ntyp,ntyp),rborn(ntyp,ntyp),sigmap1(ntyp,ntyp))
2648 allocate(sigmap2(ntyp,ntyp),sigiso2(ntyp,ntyp))
2649 allocate(chis(ntyp,ntyp),wquad(ntyp,ntyp),chipp(ntyp,ntyp))
2650 allocate(epsintab(ntyp,ntyp))
2651 allocate(dtail(2,ntyp,ntyp))
2652 allocate(alphasur(4,ntyp,ntyp),alphiso(4,ntyp,ntyp))
2653 allocate(wqdip(2,ntyp,ntyp))
2654 allocate(wstate(4,ntyp,ntyp))
2655 allocate(dhead(2,2,ntyp,ntyp))
2656 allocate(nstate(ntyp,ntyp))
2657 allocate(debaykap(ntyp,ntyp))
2659 if (.not.allocated(sigma)) allocate(sigma(0:ntyp1,0:ntyp1))
2660 if (.not.allocated(chi)) allocate(chi(ntyp1,ntyp1)) !(ntyp,ntyp)
2664 ! write (*,*) "Im in ALAB", i, " ", j
2666 eps(i,j),sigma(i,j),chi(i,j),chi(j,i),chipp(i,j),chipp(j,i), & !6 w tej linii
2667 (alphasur(k,i,j),k=1,4),sigmap1(i,j),sigmap2(i,j), & !6 w tej linii
2668 chis(i,j),chis(j,i), & !2 w tej linii
2669 nstate(i,j),(wstate(k,i,j),k=1,4), & !5 w tej lini - 1 integer pierwszy
2670 dhead(1,1,i,j),dhead(1,2,i,j),dhead(2,1,i,j),dhead(2,2,i,j),& ! 4 w tej linii
2671 dtail(1,i,j),dtail(2,i,j), & ! 2 w tej lini
2672 epshead(i,j),sig0head(i,j), & ! 2 w tej linii
2673 rborn(i,j),rborn(j,i),(wqdip(k,i,j),k=1,2),wquad(i,j), & ! 5 w tej linii
2674 alphapol(i,j),alphapol(j,i), & ! 2 w tej linii
2675 (alphiso(k,i,j),k=1,4),sigiso1(i,j),sigiso2(i,j),epsintab(i,j),debaykap(i,j) !8 w tej linii
2676 IF ((LaTeX).and.(i.gt.24)) then
2677 write (2,'(2a4,1h&,14(f8.2,1h&),23(f8.2,1h&))') restyp(i,1),restyp(j,1), &
2678 eps(i,j),sigma(i,j),chi(i,j),chi(j,i),chipp(i,j),chipp(j,i), & !6 w tej linii
2679 (alphasur(k,i,j),k=1,4),sigmap1(i,j),sigmap2(i,j), & !6 w tej linii
2680 chis(i,j),chis(j,i) !2 w tej linii
2682 ! print *,eps(i,j),sigma(i,j),"SIGMAP",i,j,sigmap1(i,j),sigmap2(j,i)
2687 IF ((LaTeX).and.(i.gt.24)) then
2688 write (2,'(2a4,1h&,14(f8.2,1h&),23(f8.2,1h&))') restyp(i,1),restyp(j,1), &
2689 dhead(1,1,i,j),dhead(2,1,i,j),& ! 2 w tej linii
2690 dtail(1,i,j),dtail(2,i,j), & ! 2 w tej lini
2691 epshead(i,j),sig0head(i,j), & ! 2 w tej linii
2692 rborn(i,j),rborn(j,i), & ! 3 w tej linii
2693 alphapol(i,j),alphapol(j,i), & ! 2 w tej linii
2694 (alphiso(k,i,j),k=1,4),sigiso1(i,j),sigiso2(i,j),epsintab(i,j),debaykap(i,j) !8 w tej linii
2701 sigma(i,j) = sigma(j,i)
2702 sigmap1(i,j)=sigmap1(j,i)
2703 sigmap2(i,j)=sigmap2(j,i)
2704 sigiso1(i,j)=sigiso1(j,i)
2705 sigiso2(i,j)=sigiso2(j,i)
2706 ! print *,"ATU",sigma(j,i),sigma(i,j),i,j
2707 nstate(i,j) = nstate(j,i)
2708 dtail(1,i,j) = dtail(1,j,i)
2709 dtail(2,i,j) = dtail(2,j,i)
2711 alphasur(k,i,j) = alphasur(k,j,i)
2712 wstate(k,i,j) = wstate(k,j,i)
2713 alphiso(k,i,j) = alphiso(k,j,i)
2716 dhead(2,1,i,j) = dhead(1,1,j,i)
2717 dhead(2,2,i,j) = dhead(1,2,j,i)
2718 dhead(1,1,i,j) = dhead(2,1,j,i)
2719 dhead(1,2,i,j) = dhead(2,2,j,i)
2721 epshead(i,j) = epshead(j,i)
2722 sig0head(i,j) = sig0head(j,i)
2725 wqdip(k,i,j) = wqdip(k,j,i)
2728 wquad(i,j) = wquad(j,i)
2729 epsintab(i,j) = epsintab(j,i)
2730 debaykap(i,j)=debaykap(j,i)
2731 ! if (epsintab(i,j).ne.1.0) print *,"WHAT?",i,j,epsintab(i,j)
2738 !--------------------- GBV potential -----------------------------------
2740 ! 40 read (isidep,*,end=117,err=117)((eps(i,j),j=i,ntyp),i=1,ntyp),&
2741 read (isidep,*,end=117,err=117)((eps(i,j),j=i,ntyp),i=1,ntyp),&
2742 (sigma0(i),i=1,ntyp),(rr0(i),i=1,ntyp),(sigii(i),i=1,ntyp),&
2743 (chip(i),i=1,ntyp),(alp(i),i=1,ntyp)
2745 write (iout,'(/a/)') 'Parameters of the GBV potential:'
2746 write (iout,'(a/)') 'The epsilon array:'
2747 call printmat(ntyp,ntyp,ntyp,iout,restyp,eps)
2748 write (iout,'(/a)') 'One-body parameters:'
2749 write (iout,'(a,4x,5a)') 'residue',' sigma ',' r0 ',&
2750 's||/s_|_^2',' chip ',' alph '
2751 write (iout,'(a3,6x,5f10.5)') (restyp(i,1),sigma0(i),rr0(i),&
2752 sigii(i),chip(i),alp(i),i=1,ntyp)
2755 write(iout,*)"Wrong ipot"
2761 !-----------------------------------------------------------------------
2762 ! Calculate the "working" parameters of SC interactions.
2764 !el from module energy - COMMON.INTERACT-------
2765 allocate(aa_aq(ntyp1,ntyp1),bb_aq(ntyp1,ntyp1))
2766 if (.not.allocated(chi)) allocate(chi(ntyp1,ntyp1)) !(ntyp,ntyp)
2767 allocate(aa_lip(ntyp1,ntyp1),bb_lip(ntyp1,ntyp1)) !(ntyp,ntyp)
2768 if (.not.allocated(sigma)) allocate(sigma(0:ntyp1,0:ntyp1))
2769 allocate(r0(ntyp1,ntyp1)) !(0:ntyp1,0:ntyp1)
2770 allocate(acavtub(ntyp1),bcavtub(ntyp1),ccavtub(ntyp1),&
2772 allocate(sc_aa_tube_par(ntyp1),sc_bb_tube_par(ntyp1),&
2778 if (scelemode.eq.0) then
2787 sc_aa_tube_par(:)=0.0d0
2788 sc_bb_tube_par(:)=0.0d0
2790 !--------------------------------
2795 epslip(i,j)=epslip(j,i)
2798 if (scelemode.eq.0) then
2801 sigma(i,j)=dsqrt(sigma0(i)**2+sigma0(j)**2)
2802 sigma(j,i)=sigma(i,j)
2803 rs0(i,j)=dwa16*sigma(i,j)
2808 if (lprint) write (iout,'(/a/10x,7a/72(1h-))') &
2809 'Working parameters of the SC interactions:',&
2810 ' a ',' b ',' augm ',' sigma ',' r0 ',&
2815 if (ipot.eq.1 .or. ipot.eq.3 .or. ipot.eq.4) then
2817 ! print *,"SIGMA ZLA?",sigma(i,j)
2825 sigeps=dsign(1.0D0,epsij)
2827 aa_aq(i,j)=epsij*rrij*rrij
2828 ! print *,"ADASKO",epsij,rrij,expon
2829 bb_aq(i,j)=-sigeps*epsij*rrij
2830 aa_aq(j,i)=aa_aq(i,j)
2831 bb_aq(j,i)=bb_aq(i,j)
2832 epsijlip=epslip(i,j)
2833 sigeps=dsign(1.0D0,epsijlip)
2834 epsijlip=dabs(epsijlip)
2835 aa_lip(i,j)=epsijlip*rrij*rrij
2836 bb_lip(i,j)=-sigeps*epsijlip*rrij
2837 aa_lip(j,i)=aa_lip(i,j)
2838 bb_lip(j,i)=bb_lip(i,j)
2839 !C write(iout,*) aa_lip
2840 if ((ipot.gt.2).and. (scelemode.eq.0)) then
2841 sigt1sq=sigma0(i)**2
2842 sigt2sq=sigma0(j)**2
2845 ratsig1=sigt2sq/sigt1sq
2846 ratsig2=1.0D0/ratsig1
2847 chi(i,j)=(sigii1-1.0D0)/(sigii1+ratsig1)
2848 if (j.gt.i) chi(j,i)=(sigii2-1.0D0)/(sigii2+ratsig2)
2849 rsum_max=dsqrt(sigii1*sigt1sq+sigii2*sigt2sq)
2853 ! if (ipot.eq.1 .or. ipot.eq.3 .or. ipot.eq.4) then
2854 sigmaii(i,j)=rsum_max
2855 sigmaii(j,i)=rsum_max
2857 ! sigmaii(i,j)=r0(i,j)
2858 ! sigmaii(j,i)=r0(i,j)
2860 !d write (iout,*) i,j,r0(i,j),sigma(i,j),rsum_max
2861 if ((ipot.eq.2 .or. ipot.eq.5) .and. r0(i,j).gt.rsum_max) then
2862 r_augm=sigma(i,j)*(rrij-sigma(i,j))/rrij
2863 augm(i,j)=epsij*r_augm**(2*expon)
2864 ! augm(i,j)=0.5D0**(2*expon)*aa(i,j)
2871 write (iout,'(2(a3,2x),3(1pe10.3),5(0pf8.3))') &
2872 restyp(i,1),restyp(j,1),aa_aq(i,j),bb_aq(i,j),augm(i,j),&
2873 sigma(i,j),r0(i,j),chi(i,j),chi(j,i)
2878 allocate(eps_nucl(ntyp_molec(2),ntyp_molec(2)))
2879 allocate(sigma_nucl(ntyp_molec(2),ntyp_molec(2))) !(ntyp_molec(2),ntyp_molec(2))
2880 allocate(elpp6_nucl(ntyp_molec(2),ntyp_molec(2))) !(ntyp_molec(2),ntyp_molec(2))
2881 allocate(elpp3_nucl(ntyp_molec(2),ntyp_molec(2))) !(ntyp,2)
2882 allocate(elpp63_nucl(ntyp_molec(2),ntyp_molec(2))) !(ntyp_molec(2),ntyp_molec(2))
2883 allocate(elpp32_nucl(ntyp_molec(2),ntyp_molec(2))) !(ntyp,2)
2884 allocate(chi_nucl(ntyp_molec(2),ntyp_molec(2)),chip_nucl(ntyp_molec(2),ntyp_molec(2))) !(ntyp_molec(2),ntyp_molec(2))
2885 allocate(ael3_nucl(ntyp_molec(2),ntyp_molec(2))) !(ntyp,2)
2886 allocate(ael6_nucl(ntyp_molec(2),ntyp_molec(2))) !(ntyp,2)
2887 allocate(ael32_nucl(ntyp_molec(2),ntyp_molec(2))) !(ntyp,2)
2888 allocate(ael63_nucl(ntyp_molec(2),ntyp_molec(2))) !(ntyp,2)
2889 allocate(aa_nucl(ntyp_molec(2),ntyp_molec(2))) !(ntyp,2)
2890 allocate(bb_nucl(ntyp_molec(2),ntyp_molec(2))) !(ntyp,2)
2891 allocate(r0_nucl(ntyp_molec(2),ntyp_molec(2))) !(ntyp,2)
2892 allocate(sigmaii_nucl(ntyp_molec(2),ntyp_molec(2))) !(ntyp_molec(2),ntyp_molec(2))
2893 allocate(eps_scp_nucl(ntyp_molec(2)),rscp_nucl(ntyp_molec(2))) !(ntyp,2)
2902 read (isidep_nucl,*) ipot_nucl
2903 ! print *,"TU?!",ipot_nucl
2904 if (ipot_nucl.eq.1) then
2905 do i=1,ntyp_molec(2)
2906 do j=i,ntyp_molec(2)
2907 read (isidep_nucl,*) eps_nucl(i,j),sigma_nucl(i,j),elpp6_nucl(i,j),&
2908 elpp3_nucl(i,j), elpp63_nucl(i,j),elpp32_nucl(i,j)
2912 do i=1,ntyp_molec(2)
2913 do j=i,ntyp_molec(2)
2914 read (isidep_nucl,*) eps_nucl(i,j),sigma_nucl(i,j),chi_nucl(i,j),&
2915 chi_nucl(j,i),chip_nucl(i,j),chip_nucl(j,i),&
2916 elpp6_nucl(i,j),elpp3_nucl(i,j),elpp63_nucl(i,j),elpp32_nucl(i,j)
2920 ! rpp(1,1)=2**(1.0/6.0)*5.16158
2921 do i=1,ntyp_molec(2)
2922 do j=i,ntyp_molec(2)
2923 rrij=sigma_nucl(i,j)
2927 epsij=4*eps_nucl(i,j)
2928 sigeps=dsign(1.0D0,epsij)
2930 aa_nucl(i,j)=epsij*rrij*rrij
2931 bb_nucl(i,j)=-sigeps*epsij*rrij
2932 ael3_nucl(i,j)=elpp3_nucl(i,j)*dsqrt(rrij)
2933 ael6_nucl(i,j)=elpp6_nucl(i,j)*rrij
2934 ael63_nucl(i,j)=elpp63_nucl(i,j)*rrij
2935 ael32_nucl(i,j)=elpp32_nucl(i,j)*rrij
2936 sigmaii_nucl(i,j)=sigma_nucl(i,j)/sqrt(1-(chi_nucl(i,j)+chi_nucl(j,i)- &
2937 2*chi_nucl(i,j)*chi_nucl(j,i))/(1-chi_nucl(i,j)*chi_nucl(j,i)))
2940 aa_nucl(i,j)=aa_nucl(j,i)
2941 bb_nucl(i,j)=bb_nucl(j,i)
2942 ael3_nucl(i,j)=ael3_nucl(j,i)
2943 ael6_nucl(i,j)=ael6_nucl(j,i)
2944 ael63_nucl(i,j)=ael63_nucl(j,i)
2945 ael32_nucl(i,j)=ael32_nucl(j,i)
2946 elpp3_nucl(i,j)=elpp3_nucl(j,i)
2947 elpp6_nucl(i,j)=elpp6_nucl(j,i)
2948 elpp63_nucl(i,j)=elpp63_nucl(j,i)
2949 elpp32_nucl(i,j)=elpp32_nucl(j,i)
2950 eps_nucl(i,j)=eps_nucl(j,i)
2951 sigma_nucl(i,j)=sigma_nucl(j,i)
2952 sigmaii_nucl(i,j)=sigmaii_nucl(j,i)
2956 write(iout,*) "tube param"
2957 read(itube,*) epspeptube,sigmapeptube,acavtubpep,bcavtubpep, &
2958 ccavtubpep,dcavtubpep,tubetranenepep
2959 sigmapeptube=sigmapeptube**6
2960 sigeps=dsign(1.0D0,epspeptube)
2961 epspeptube=dabs(epspeptube)
2962 pep_aa_tube=4.0d0*epspeptube*sigmapeptube**2
2963 pep_bb_tube=-sigeps*4.0d0*epspeptube*sigmapeptube
2964 write(iout,*) pep_aa_tube,pep_bb_tube,tubetranenepep
2966 read(itube,*) epssctube,sigmasctube,acavtub(i),bcavtub(i), &
2967 ccavtub(i),dcavtub(i),tubetranene(i)
2968 sigmasctube=sigmasctube**6
2969 sigeps=dsign(1.0D0,epssctube)
2970 epssctube=dabs(epssctube)
2971 sc_aa_tube_par(i)=4.0d0*epssctube*sigmasctube**2
2972 sc_bb_tube_par(i)=-sigeps*4.0d0*epssctube*sigmasctube
2973 write(iout,*) sc_aa_tube_par(i), sc_bb_tube_par(i),tubetranene(i)
2975 !-----------------READING SC BASE POTENTIALS-----------------------------
2976 allocate(eps_scbase(ntyp_molec(1),ntyp_molec(2)))
2977 allocate(sigma_scbase(ntyp_molec(1),ntyp_molec(2)))
2978 allocate(chi_scbase(ntyp_molec(1),ntyp_molec(2),2))
2979 allocate(chipp_scbase(ntyp_molec(1),ntyp_molec(2),2))
2980 allocate(alphasur_scbase(4,ntyp_molec(1),ntyp_molec(2)))
2981 allocate(sigmap1_scbase(ntyp_molec(1),ntyp_molec(2)))
2982 allocate(sigmap2_scbase(ntyp_molec(1),ntyp_molec(2)))
2983 allocate(chis_scbase(ntyp_molec(1),ntyp_molec(2),2))
2984 allocate(dhead_scbasei(ntyp_molec(1),ntyp_molec(2)))
2985 allocate(dhead_scbasej(ntyp_molec(1),ntyp_molec(2)))
2986 allocate(rborn_scbasei(ntyp_molec(1),ntyp_molec(2)))
2987 allocate(rborn_scbasej(ntyp_molec(1),ntyp_molec(2)))
2988 allocate(wdipdip_scbase(3,ntyp_molec(1),ntyp_molec(2)))
2989 allocate(wqdip_scbase(2,ntyp_molec(1),ntyp_molec(2)))
2990 allocate(alphapol_scbase(ntyp_molec(1),ntyp_molec(2)))
2991 allocate(epsintab_scbase(ntyp_molec(1),ntyp_molec(2)))
2994 do i=1,ntyp_molec(1)
2995 do j=1,ntyp_molec(2)-1 ! without U then we will take T for U
2996 write (*,*) "Im in ", i, " ", j
2997 read(isidep_scbase,*) &
2998 eps_scbase(i,j),sigma_scbase(i,j),chi_scbase(i,j,1),&
2999 chi_scbase(i,j,2),chipp_scbase(i,j,1),chipp_scbase(i,j,2)
3000 write(*,*) "eps",eps_scbase(i,j)
3001 read(isidep_scbase,*) &
3002 (alphasur_scbase(k,i,j),k=1,4),sigmap1_scbase(i,j),sigmap2_scbase(i,j), &
3003 chis_scbase(i,j,1),chis_scbase(i,j,2)
3004 read(isidep_scbase,*) &
3005 dhead_scbasei(i,j), &
3006 dhead_scbasej(i,j), &
3007 rborn_scbasei(i,j),rborn_scbasej(i,j)
3008 read(isidep_scbase,*) &
3009 (wdipdip_scbase(k,i,j),k=1,3), &
3010 (wqdip_scbase(k,i,j),k=1,2)
3011 read(isidep_scbase,*) &
3012 alphapol_scbase(i,j), &
3013 epsintab_scbase(i,j)
3016 allocate(aa_scbase(ntyp_molec(1),ntyp_molec(2)))
3017 allocate(bb_scbase(ntyp_molec(1),ntyp_molec(2)))
3019 do i=1,ntyp_molec(1)
3020 do j=1,ntyp_molec(2)-1
3021 epsij=eps_scbase(i,j)
3022 rrij=sigma_scbase(i,j)
3027 sigeps=dsign(1.0D0,epsij)
3029 aa_scbase(i,j)=epsij*rrij*rrij
3030 bb_scbase(i,j)=-sigeps*epsij*rrij
3033 !-----------------READING PEP BASE POTENTIALS-------------------
3034 allocate(eps_pepbase(ntyp_molec(2)))
3035 allocate(sigma_pepbase(ntyp_molec(2)))
3036 allocate(chi_pepbase(ntyp_molec(2),2))
3037 allocate(chipp_pepbase(ntyp_molec(2),2))
3038 allocate(alphasur_pepbase(4,ntyp_molec(2)))
3039 allocate(sigmap1_pepbase(ntyp_molec(2)))
3040 allocate(sigmap2_pepbase(ntyp_molec(2)))
3041 allocate(chis_pepbase(ntyp_molec(2),2))
3042 allocate(wdipdip_pepbase(3,ntyp_molec(2)))
3045 do j=1,ntyp_molec(2)-1 ! without U then we will take T for U
3046 write (*,*) "Im in ", i, " ", j
3047 read(isidep_pepbase,*) &
3048 eps_pepbase(j),sigma_pepbase(j),chi_pepbase(j,1),&
3049 chi_pepbase(j,2),chipp_pepbase(j,1),chipp_pepbase(j,2)
3050 write(*,*) "eps",eps_pepbase(j)
3051 read(isidep_pepbase,*) &
3052 (alphasur_pepbase(k,j),k=1,4),sigmap1_pepbase(j),sigmap2_pepbase(j), &
3053 chis_pepbase(j,1),chis_pepbase(j,2)
3054 read(isidep_pepbase,*) &
3055 (wdipdip_pepbase(k,j),k=1,3)
3057 allocate(aa_pepbase(ntyp_molec(2)))
3058 allocate(bb_pepbase(ntyp_molec(2)))
3060 do j=1,ntyp_molec(2)-1
3061 epsij=eps_pepbase(j)
3062 rrij=sigma_pepbase(j)
3067 sigeps=dsign(1.0D0,epsij)
3069 aa_pepbase(j)=epsij*rrij*rrij
3070 bb_pepbase(j)=-sigeps*epsij*rrij
3072 !--------------READING SC PHOSPHATE-------------------------------------
3073 allocate(eps_scpho(ntyp_molec(1)))
3074 allocate(sigma_scpho(ntyp_molec(1)))
3075 allocate(chi_scpho(ntyp_molec(1),2))
3076 allocate(chipp_scpho(ntyp_molec(1),2))
3077 allocate(alphasur_scpho(4,ntyp_molec(1)))
3078 allocate(sigmap1_scpho(ntyp_molec(1)))
3079 allocate(sigmap2_scpho(ntyp_molec(1)))
3080 allocate(chis_scpho(ntyp_molec(1),2))
3081 allocate(wqq_scpho(ntyp_molec(1)))
3082 allocate(wqdip_scpho(2,ntyp_molec(1)))
3083 allocate(alphapol_scpho(ntyp_molec(1)))
3084 allocate(epsintab_scpho(ntyp_molec(1)))
3085 allocate(dhead_scphoi(ntyp_molec(1)))
3086 allocate(rborn_scphoi(ntyp_molec(1)))
3087 allocate(rborn_scphoj(ntyp_molec(1)))
3088 allocate(alphi_scpho(ntyp_molec(1)))
3092 do j=1,ntyp_molec(1) ! without U then we will take T for U
3093 write (*,*) "Im in scpho ", i, " ", j
3094 read(isidep_scpho,*) &
3095 eps_scpho(j),sigma_scpho(j),chi_scpho(j,1),&
3096 chi_scpho(j,2),chipp_scpho(j,1),chipp_scpho(j,2)
3097 write(*,*) "eps",eps_scpho(j)
3098 read(isidep_scpho,*) &
3099 (alphasur_scpho(k,j),k=1,4),sigmap1_scpho(j),sigmap2_scpho(j), &
3100 chis_scpho(j,1),chis_scpho(j,2)
3101 read(isidep_scpho,*) &
3102 (wqdip_scpho(k,j),k=1,2),wqq_scpho(j),dhead_scphoi(j)
3103 read(isidep_scpho,*) &
3104 epsintab_scpho(j),alphapol_scpho(j),rborn_scphoi(j),rborn_scphoj(j), &
3108 allocate(aa_scpho(ntyp_molec(1)))
3109 allocate(bb_scpho(ntyp_molec(1)))
3111 do j=1,ntyp_molec(1)
3118 sigeps=dsign(1.0D0,epsij)
3120 aa_scpho(j)=epsij*rrij*rrij
3121 bb_scpho(j)=-sigeps*epsij*rrij
3125 read(isidep_peppho,*) &
3126 eps_peppho,sigma_peppho
3127 read(isidep_peppho,*) &
3128 (alphasur_peppho(k),k=1,4),sigmap1_peppho,sigmap2_peppho
3129 read(isidep_peppho,*) &
3130 (wqdip_peppho(k),k=1,2)
3138 sigeps=dsign(1.0D0,epsij)
3140 aa_peppho=epsij*rrij*rrij
3141 bb_peppho=-sigeps*epsij*rrij
3144 allocate(aad(ntyp,2),bad(ntyp,2)) !(ntyp,2)
3149 ! Define the SC-p interaction constants (hard-coded; old style)
3152 ! "Soft" SC-p repulsion (causes helices to be too flat, but facilitates
3154 ! aad(i,1)=0.3D0*4.0D0**12
3155 ! Following line for constants currently implemented
3156 ! "Hard" SC-p repulsion (gives correct turn spacing in helices)
3157 aad(i,1)=1.5D0*4.0D0**12
3158 ! aad(i,1)=0.17D0*5.6D0**12
3160 ! "Soft" SC-p repulsion
3162 ! Following line for constants currently implemented
3163 ! aad(i,1)=0.3D0*4.0D0**6
3164 ! "Hard" SC-p repulsion
3165 bad(i,1)=3.0D0*4.0D0**6
3166 ! bad(i,1)=-2.0D0*0.17D0*5.6D0**6
3175 ! 8/9/01 Read the SC-p interaction constants from file
3178 read (iscpp,*,end=118,err=118) (eps_scp(i,j),rscp(i,j),j=1,2)
3181 aad(i,1)=dabs(eps_scp(i,1))*rscp(i,1)**12
3182 aad(i,2)=dabs(eps_scp(i,2))*rscp(i,2)**12
3183 bad(i,1)=-2*eps_scp(i,1)*rscp(i,1)**6
3184 bad(i,2)=-2*eps_scp(i,2)*rscp(i,2)**6
3188 write (iout,*) "Parameters of SC-p interactions:"
3190 write (iout,'(4f8.3,4e12.4)') eps_scp(i,1),rscp(i,1),&
3191 eps_scp(i,2),rscp(i,2),aad(i,1),bad(i,1),aad(i,2),bad(i,2)
3196 allocate(aad_nucl(ntyp_molec(2)),bad_nucl(ntyp_molec(2))) !(ntyp,2)
3198 do i=1,ntyp_molec(2)
3199 read (iscpp_nucl,*,end=118,err=118) eps_scp_nucl(i),rscp_nucl(i)
3201 do i=1,ntyp_molec(2)
3202 aad_nucl(i)=dabs(eps_scp_nucl(i))*rscp_nucl(i)**12
3203 bad_nucl(i)=-2*eps_scp_nucl(i)*rscp_nucl(i)**6
3205 r0pp=1.12246204830937298142*5.16158
3211 ! Define the constants of the disulfide bridge
3215 ! Old arbitrary potential - commented out.
3220 ! Constants of the disulfide-bond potential determined based on the RHF/6-31G**
3221 ! energy surface of diethyl disulfide.
3222 ! A. Liwo and U. Kozlowska, 11/24/03
3240 allocate(alphapolcat(ntyp,ntyp),epsheadcat(ntyp,ntyp),sig0headcat(ntyp,ntyp))
3241 allocate(sigiso1cat(ntyp,ntyp),rborncat(ntyp,ntyp),sigmap1cat(ntyp,ntyp))
3242 allocate(sigmap2cat(ntyp,ntyp),sigiso2cat(ntyp,ntyp))
3243 allocate(chiscat(ntyp,ntyp),wquadcat(ntyp,ntyp),chippcat(ntyp,ntyp))
3244 allocate(epsintabcat(ntyp,ntyp))
3245 allocate(dtailcat(2,ntyp,ntyp))
3246 allocate(alphasurcat(4,ntyp,ntyp),alphisocat(4,ntyp,ntyp))
3247 allocate(wqdipcat(2,ntyp,ntyp))
3248 allocate(wstatecat(4,ntyp,ntyp))
3249 allocate(dheadcat(2,2,ntyp,ntyp))
3250 allocate(nstatecat(ntyp,ntyp))
3251 allocate(debaykapcat(ntyp,ntyp))
3253 if (.not.allocated(epscat)) allocate (epscat(0:ntyp1,0:ntyp1))
3254 if (.not.allocated(sigmacat)) allocate(sigmacat(0:ntyp1,0:ntyp1))
3255 if (.not.allocated(chicat)) allocate(chicat(ntyp1,ntyp1)) !(ntyp,ntyp)
3256 allocate (ichargecat(ntyp_molec(5)))
3257 ! i to SC, j to jon, isideocat - nazwa pliku z ktorego czytam parametry
3258 if (oldion.eq.0) then
3259 if (.not.allocated(icharge)) then ! this mean you are oprating in old sc-sc mode
3260 allocate(icharge(1:ntyp1))
3261 read(iion,*) (icharge(i),i=1,ntyp)
3266 do i=1,ntyp_molec(5)
3267 read(iion,*) msc(i,5),restok(i,5),ichargecat(i)
3268 print *,msc(i,5),restok(i,5)
3273 do j=1,ntyp_molec(5)
3274 ! write (*,*) "Im in ALAB", i, " ", j
3276 epscat(i,j),sigmacat(i,j),chicat(i,j),chicat(j,i),chippcat(i,j),chippcat(j,i), &
3277 (alphasurcat(k,i,j),k=1,4),sigmap1cat(i,j),sigmap2cat(i,j),&
3278 chiscat(i,j),chiscat(j,i), &
3279 nstatecat(i,j),(wstatecat(k,i,j),k=1,4), & !5 w tej lini - 1 integer pierwszy
3280 dheadcat(1,1,i,j),dheadcat(1,2,i,j),dheadcat(2,1,i,j),dheadcat(2,2,i,j),&
3281 dtailcat(1,i,j),dtailcat(2,i,j), &
3282 epsheadcat(i,j),sig0headcat(i,j), &
3284 rborncat(i,j),rborncat(j,i),(wqdipcat(k,i,j),k=1,2), &
3285 alphapolcat(i,j),alphapolcat(j,i), &
3286 (alphisocat(k,i,j),k=1,4),sigiso1cat(i,j),sigiso2cat(i,j),epsintabcat(i,j),debaykapcat(i,j)
3287 ! print *,eps(i,j),sigma(i,j),"SIGMAP",i,j,sigmap1(i,j),sigmap2(j,i)
3290 allocate(aa_aq_cat(-ntyp:ntyp,ntyp),bb_aq_cat(-ntyp:ntyp,ntyp))
3292 do j=1,ntyp_molec(5)
3295 sigeps=dsign(1.0D0,epsij)
3297 aa_aq_cat(i,j)=epsij*rrij*rrij
3298 bb_aq_cat(i,j)=-sigeps*epsij*rrij
3305 write (iout,'(/a)') "Disulfide bridge parameters:"
3306 write (iout,'(a,f10.2)') 'S-S bridge energy: ',ebr
3307 write (iout,'(2(a,f10.2))') 'd0cm:',d0cm,' akcm:',akcm
3308 write (iout,'(2(a,f10.2))') 'akth:',akth,' akct:',akct
3309 write (iout,'(3(a,f10.2))') 'v1ss:',v1ss,' v2ss:',v2ss,&
3312 if (shield_mode.gt.0) then
3313 pi=4.0D0*datan(1.0D0)
3314 !C VSolvSphere the volume of solving sphere
3316 !C rpp(1,1) is the energy r0 for peptide group contact and will be used for it
3317 !C there will be no distinction between proline peptide group and normal peptide
3318 !C group in case of shielding parameters
3319 VSolvSphere=4.0/3.0*pi*(4.50d0)**3
3320 VSolvSphere_div=VSolvSphere-4.0/3.0*pi*(4.50/2.0)**3
3321 write (iout,*) VSolvSphere,VSolvSphere_div
3322 !C long axis of side chain
3324 long_r_sidechain(i)=vbldsc0(1,i)
3325 ! if (scelemode.eq.0) then
3326 short_r_sidechain(i)=sigma(i,i)/sqrt(2.0)
3327 if (short_r_sidechain(i).eq.0.0) short_r_sidechain(i)=0.2
3329 ! short_r_sidechain(i)=sigma(i,i)
3331 write(iout,*) "parame for long and short axis",i,vbldsc0(1,i),&
3338 111 write (iout,*) "Error reading bending energy parameters."
3340 112 write (iout,*) "Error reading rotamer energy parameters."
3342 113 write (iout,*) "Error reading torsional energy parameters."
3344 114 write (iout,*) "Error reading double torsional energy parameters."
3346 115 write (iout,*) &
3347 "Error reading cumulant (multibody energy) parameters."
3349 116 write (iout,*) "Error reading electrostatic energy parameters."
3351 117 write (iout,*) "Error reading side chain interaction parameters."
3353 118 write (iout,*) "Error reading SCp interaction parameters."
3355 119 write (iout,*) "Error reading SCCOR parameters"
3357 121 write (iout,*) "Error in Czybyshev parameters"
3360 call MPI_Finalize(Ierror)
3364 end subroutine parmread
3366 !-----------------------------------------------------------------------------
3368 !-----------------------------------------------------------------------------
3369 subroutine printmat(ldim,m,n,iout,key,a)
3372 character(len=3),dimension(n) :: key
3373 real(kind=8),dimension(ldim,n) :: a
3375 integer :: i,j,k,m,iout,nlim
3379 write (iout,1000) (key(k),k=i,nlim)
3381 1000 format (/5x,8(6x,a3))
3382 1020 format (/80(1h-)/)
3384 write (iout,1010) key(j),(a(j,k),k=i,nlim)
3387 1010 format (a3,2x,8(f9.4))
3389 end subroutine printmat
3390 !-----------------------------------------------------------------------------
3392 !-----------------------------------------------------------------------------
3394 ! Read the PDB file and convert the peptide geometry into virtual-chain
3397 use energy_data, only: itype,istype
3401 ! use control, only: rescode,sugarcode
3402 ! implicit real*8 (a-h,o-z)
3403 ! include 'DIMENSIONS'
3404 ! include 'COMMON.LOCAL'
3405 ! include 'COMMON.VAR'
3406 ! include 'COMMON.CHAIN'
3407 ! include 'COMMON.INTERACT'
3408 ! include 'COMMON.IOUNITS'
3409 ! include 'COMMON.GEO'
3410 ! include 'COMMON.NAMES'
3411 ! include 'COMMON.CONTROL'
3412 ! include 'COMMON.DISTFIT'
3413 ! include 'COMMON.SETUP'
3414 integer :: i,j,ibeg,ishift1,ires,iii,ires_old,ishift,k!,ity!,&
3416 logical :: lprn=.true.,fail
3417 real(kind=8),dimension(3) :: e1,e2,e3
3418 real(kind=8) :: dcj,efree_temp
3419 character(len=3) :: seq,res,res2
3420 character(len=5) :: atom
3421 character(len=80) :: card
3422 real(kind=8),dimension(3,20) :: sccor
3423 integer :: kkk,lll,icha,kupa,molecule,counter,seqalingbegin !rescode,
3424 integer :: isugar,molecprev,firstion
3425 character*1 :: sugar
3427 real(kind=8),dimension(3) :: ccc
3429 integer,dimension(2,maxres/3) :: hfrag_alloc
3430 integer,dimension(4,maxres/3) :: bfrag_alloc
3431 real(kind=8),dimension(3,maxres2+2,maxperm) :: cref_alloc !(3,maxres2+2,maxperm)
3432 real(kind=8),dimension(:,:), allocatable :: c_temporary
3433 integer,dimension(:,:) , allocatable :: itype_temporary
3434 integer,dimension(:),allocatable :: istype_temp
3441 ! write (2,*) "UNRES_PDB",unres_pdb
3461 !-----------------------------
3462 allocate(hfrag(2,maxres/3)) !(2,maxres/3)
3463 allocate(bfrag(4,maxres/3)) !(4,maxres/3)
3464 if(.not. allocated(istype)) allocate(istype(maxres))
3466 read (ipdbin,'(a80)',end=10) card
3467 write (iout,'(a)') card
3468 if (card(:5).eq.'HELIX') then
3471 read(card(22:25),*) hfrag(1,nhfrag)
3472 read(card(34:37),*) hfrag(2,nhfrag)
3474 if (card(:5).eq.'SHEET') then
3477 read(card(24:26),*) bfrag(1,nbfrag)
3478 read(card(35:37),*) bfrag(2,nbfrag)
3479 !rc----------------------------------------
3480 !rc to be corrected !!!
3481 bfrag(3,nbfrag)=bfrag(1,nbfrag)
3482 bfrag(4,nbfrag)=bfrag(2,nbfrag)
3483 !rc----------------------------------------
3485 if (card(:3).eq.'END') then
3487 else if (card(:3).eq.'TER') then
3492 itype(ires_old,molecule)=ntyp1_molec(molecule)
3493 itype(ires_old-1,molecule)=ntyp1_molec(molecule)
3494 nres_molec(molecule)=nres_molec(molecule)+2
3496 ! write (iout,*) "Chain ended",ires,ishift,ires_old
3499 dc(j,ires)=sccor(j,iii)
3502 call sccenter(ires,iii,sccor)
3508 if (index(card,"FREE ENERGY").gt.0) read(card(35:),*) efree_temp
3509 ! Fish out the ATOM cards.
3510 ! write(iout,*) 'card',card(1:20)
3511 ! print *,"ATU ",card(1:6), CARD(3:6)
3513 if (index(card(1:4),'ATOM').gt.0) then
3514 read (card(12:16),*) atom
3515 ! write (iout,*) "! ",atom," !",ires
3516 ! if (atom.eq.'CA' .or. atom.eq.'CH3') then
3517 read (card(23:26),*) ires
3518 read (card(18:20),'(a3)') res
3519 ! write (iout,*) "ires",ires,ires-ishift+ishift1,
3520 ! & " ires_old",ires_old
3521 ! write (iout,*) "ishift",ishift," ishift1",ishift1
3522 ! write (iout,*) "IRES",ires-ishift+ishift1,ires_old
3523 if (ires-ishift+ishift1.ne.ires_old) then
3524 ! Calculate the CM of the preceding residue.
3525 ! if (ibeg.eq.0) call sccenter(ires,iii,sccor)
3527 ! write (iout,*) "Calculating sidechain center iii",iii
3530 dc(j,ires+ishift1-ishift-1)=sccor(j,iii)
3533 call sccenter(ires_old,iii,sccor)
3537 ! Start new residue.
3538 if (res.eq.'Cl-' .or. res.eq.'Na+') then
3541 else if (ibeg.eq.1) then
3542 write (iout,*) "BEG ires",ires
3544 if (res.ne.'GLY' .and. res.ne. 'ACE') then
3547 nres_molec(molecule)=nres_molec(molecule)+1
3549 ires=ires-ishift+ishift1
3551 ! write (iout,*) "ishift",ishift," ires",ires,&
3552 ! " ires_old",ires_old
3554 else if (ibeg.eq.2) then
3556 ishift=-ires_old+ires-1 !!!!!
3557 ishift1=ishift1-1 !!!!!
3558 ! write (iout,*) "New chain started",ires,ishift,ishift1,"!"
3559 ires=ires-ishift+ishift1
3560 ! print *,ires,ishift,ishift1
3564 ishift=ishift-(ires-ishift+ishift1-ires_old-1)
3565 ires=ires-ishift+ishift1
3568 ! print *,'atom',ires,atom
3569 if (res.eq.'ACE' .or. res.eq.'NHE') then
3572 if (atom.eq.'CA '.or.atom.eq.'N ') then
3574 itype(ires,molecule)=rescode(ires,res,0,molecule)
3576 ! nres_molec(molecule)=nres_molec(molecule)+1
3580 itype(ires,molecule)=rescode(ires,res2,0,molecule)
3581 ! nres_molec(molecule)=nres_molec(molecule)+1
3582 read (card(19:19),'(a1)') sugar
3583 isugar=sugarcode(sugar,ires)
3584 ! if (ibeg.eq.1) then
3588 ! print *,"ires=",ires,istype(ires)
3594 ires=ires-ishift+ishift1
3596 ! write (iout,*) "ires_old",ires_old," ires",ires
3597 if (card(27:27).eq."A" .or. card(27:27).eq."B") then
3600 ! write (2,*) "ires",ires," res ",res!," ity"!,ity
3601 if (atom.eq.'CA' .or. atom.eq.'CH3' .or. &
3602 res.eq.'NHE'.and.atom(:2).eq.'HN') then
3603 read(card(31:54),'(3f8.3)') (c(j,ires),j=1,3)
3604 ! print *,ires,ishift,ishift1
3605 ! write (iout,*) "backbone ",atom
3607 write (iout,'(2i3,2x,a,3f8.3)') &
3608 ires,itype(ires,1),res,(c(j,ires),j=1,3)
3611 nres_molec(molecule)=nres_molec(molecule)+1
3613 sccor(j,iii)=c(j,ires)
3615 else if (.not.unres_pdb .and. (atom.eq."C1'" .or. &
3616 atom.eq."C2'" .or. atom.eq."C3'" &
3617 .or. atom.eq."C4'" .or. atom.eq."O4'")) then
3618 read(card(31:54),'(3f8.3)') (ccc(j),j=1,3)
3619 !c write (2,'(i5,3f10.5)') ires,(ccc(j),j=1,3)
3620 ! print *,ires,ishift,ishift1
3624 ! sccor(j,iii)=c(j,ires)
3627 c(j,ires)=c(j,ires)+ccc(j)/5.0
3629 print *,counter,molecule
3630 if (counter.eq.5) then
3632 nres_molec(molecule)=nres_molec(molecule)+1
3635 ! sccor(j,iii)=c(j,ires)
3639 ! print *, "ATOM",atom(1:3)
3640 else if (atom.eq."C5'") then
3641 read (card(19:19),'(a1)') sugar
3642 isugar=sugarcode(sugar,ires)
3647 ! print *,ires,istype(ires)
3651 ! print *,"nres_molec(molecule)",nres_molec(molecule),ires
3652 read(card(31:54),'(3f8.3)') (c(j,ires),j=1,3)
3653 nres_molec(molecule)=nres_molec(molecule)+1
3654 print *,"nres_molec(molecule)",nres_molec(molecule),ires
3658 read(card(31:54),'(3f8.3)') (sccor(j,iii),j=1,3)
3660 else if ((atom.eq."C1'").and.unres_pdb) then
3662 read(card(31:54),'(3f8.3)') (sccor(j,iii),j=1,3)
3663 ! write (*,*) card(23:27),ires,itype(ires,1)
3664 else if (atom.ne.'O'.and.atom(1:1).ne.'H' .and. &
3665 atom.ne.'N' .and. atom.ne.'C' .and. &
3666 atom(:2).ne.'1H' .and. atom(:2).ne.'2H' .and. &
3667 atom.ne.'OXT' .and. atom(:2).ne.'3H' &
3668 .and. atom.ne.'P '.and. &
3669 atom(1:1).ne.'H' .and. &
3670 atom.ne.'OP1' .and. atom.ne.'OP2 '.and. atom.ne.'OP3'&
3672 ! write (iout,*) "sidechain ",atom
3673 ! write (iout,*) "sidechain ",atom,molecule,ires,atom(3:3)
3674 if ((molecule.ne.2).or.(atom(3:3).ne."'")) then
3675 ! write (iout,*) "sidechain ",atom,molecule,ires,atom(3:3)
3677 read(card(31:54),'(3f8.3)') (sccor(j,iii),j=1,3)
3680 ! print *,"IONS",ions,card(1:6)
3681 else if ((ions).and.(card(1:6).eq.'HETATM')) then
3682 if (firstion.eq.0) then
3686 dc(j,ires)=sccor(j,iii)
3689 call sccenter(ires,iii,sccor)
3692 read (card(12:16),*) atom
3693 ! print *,"HETATOM", atom
3694 read (card(18:20),'(a3)') res
3695 if ((atom(1:2).eq.'NA').or.(atom(1:2).eq.'CL').or.&
3696 (atom(1:2).eq.'CA').or.(atom(1:2).eq.'MG') &
3697 .or.(atom(1:2).eq.'K ')) &
3700 if (molecule.ne.5) molecprev=molecule
3702 nres_molec(molecule)=nres_molec(molecule)+1
3703 print *,"HERE",nres_molec(molecule)
3705 itype(ires,molecule)=rescode(ires,res,0,molecule)
3706 read(card(31:54),'(3f8.3)') (c(j,ires),j=1,3)
3710 10 write (iout,'(a,i5)') ' Number of residues found: ',ires
3711 if (ires.eq.0) return
3712 ! Calculate dummy residue coordinates inside the "chain" of a multichain
3715 if (((ires_old.ne.ires).and.(molecule.ne.5)) &
3717 nres_molec(molecule)=nres_molec(molecule)-2
3718 print *,'I have',nres, nres_molec(:)
3720 do k=1,4 ! ions are without dummy
3721 if (nres_molec(k).eq.0) cycle
3723 ! write (iout,*) i,itype(i,1)
3724 ! if (itype(i,1).eq.ntyp1) then
3725 ! write (iout,*) "dummy",i,itype(i,1)
3727 ! c(j,i)=((c(j,i-1)+c(j,i+1))/2+2*c(j,i-1)-c(j,i-2))/2
3728 ! c(j,i)=(c(j,i-1)+c(j,i+1))/2
3732 if (itype(i,k).eq.ntyp1_molec(k)) then
3733 if (itype(i+1,k).eq.ntyp1_molec(k)) then
3734 if (itype(i+2,k).eq.0) then
3735 ! print *,"masz sieczke"
3737 if (itype(i+2,j).ne.0) then
3739 itype(i+1,j)=ntyp1_molec(j)
3740 nres_molec(k)=nres_molec(k)-1
3741 nres_molec(j)=nres_molec(j)+1
3747 ! 16/01/2014 by Adasko: Adding to dummy atoms in the chain
3748 ! first is connected prevous chain (itype(i+1,1).eq.ntyp1)=true
3749 ! second dummy atom is conected to next chain itype(i+1,1).eq.ntyp1=false
3750 ! if (unres_pdb) then
3751 ! 2/15/2013 by Adam: corrected insertion of the last dummy residue
3752 ! print *,i,'tu dochodze'
3753 ! call refsys(i-3,i-2,i-1,e1,e2,e3,fail)
3761 ! c(j,i)=c(j,i-1)-1.9d0*e2(j)
3765 dcj=(c(j,i-2)-c(j,i-3))/2.0
3766 if (dcj.eq.0) dcj=1.23591524223
3771 else !itype(i+1,1).eq.ntyp1
3772 ! if (unres_pdb) then
3773 ! 2/15/2013 by Adam: corrected insertion of the first dummy residue
3774 ! call refsys(i+1,i+2,i+3,e1,e2,e3,fail)
3781 ! c(j,i)=c(j,i+1)-1.9d0*e2(j)
3782 c(j,i)=c(j,i-1)+1.9d0*(-e1(j)+e2(j))/sqrt(2.0d0)
3786 dcj=(c(j,i+3)-c(j,i+2))/2.0
3787 if (dcj.eq.0) dcj=1.23591524223
3792 endif !itype(i+1,1).eq.ntyp1
3793 endif !itype.eq.ntyp1
3797 ! Calculate the CM of the last side chain.
3801 dc(j,ires)=sccor(j,iii)
3804 call sccenter(ires,iii,sccor)
3810 ! print *,"molecule",molecule
3811 if ((itype(nres,1).ne.10)) then
3813 if (molecule.eq.5) molecule=molecprev
3814 itype(nres,molecule)=ntyp1_molec(molecule)
3815 nres_molec(molecule)=nres_molec(molecule)+1
3816 ! if (unres_pdb) then
3817 ! 2/15/2013 by Adam: corrected insertion of the last dummy residue
3818 ! call refsys(nres-3,nres-2,nres-1,e1,e2,e3,fail)
3825 ! c(j,nres)=c(j,nres-1)-1.9d0*e2(j)
3829 dcj=(c(j,nres-2)-c(j,nres-3))/2.0
3830 c(j,nres)=c(j,nres-1)+dcj
3831 c(j,2*nres)=c(j,nres)
3835 ! print *,'I have',nres, nres_molec(:)
3837 !el kontrola nres w pliku inputowym WHAM-a w porownaniu z wartoscia wczytana z pliku pdb
3839 if (nres.ne.nres0) then
3840 write (iout,*) "Error: wrong parameter value: NRES=",nres,&
3842 stop "Error nres value in WHAM input"
3845 !---------------------------------
3846 !el reallocate tables
3849 ! hfrag_alloc(j,i)=hfrag(j,i)
3852 ! bfrag_alloc(j,i)=bfrag(j,i)
3858 ! allocate(hfrag(2,nres/3)) !(2,maxres/3)
3859 !el allocate(hfrag(2,nhfrag)) !(2,maxres/3)
3860 !el allocate(bfrag(4,nbfrag)) !(4,maxres/3)
3861 ! allocate(bfrag(4,nres/3)) !(4,maxres/3)
3865 ! hfrag(j,i)=hfrag_alloc(j,i)
3870 ! bfrag(j,i)=bfrag_alloc(j,i)
3873 !el end reallocate tables
3874 !---------------------------------
3882 c(j,2*nres)=c(j,nres)
3885 if (itype(1,1).eq.ntyp1) then
3889 ! 2/15/2013 by Adam: corrected insertion of the first dummy residue
3890 call refsys(2,3,4,e1,e2,e3,fail)
3897 ! c(j,1)=c(j,2)-1.9d0*e2(j)
3898 c(j,1)=c(j,2)+1.9d0*(e1(j)-e2(j))/sqrt(2.0d0)
3902 dcj=(c(j,4)-c(j,3))/2.0
3908 ! First lets assign correct dummy to correct type of chain
3910 if (itype(1,1).eq.ntyp1) then
3911 if (itype(2,1).eq.0) then
3913 if (itype(2,j).ne.0) then
3915 itype(1,j)=ntyp1_molec(j)
3916 nres_molec(1)=nres_molec(1)-1
3917 nres_molec(j)=nres_molec(j)+1
3924 print *,'I have',nres, nres_molec(:)
3926 ! Copy the coordinates to reference coordinates
3932 ! Calculate internal coordinates.
3934 write (iout,'(/a)') &
3935 "Cartesian coordinates of the reference structure"
3936 write (iout,'(a,16x,3(3x,a5),5x,3(3x,a5))') &
3937 "Residue","X(CA)","Y(CA)","Z(CA)","X(SC)","Y(SC)","Z(SC)"
3939 write (iout,'(5(a3,1x),i5,3f8.3,5x,3f8.3)') &
3940 (restyp(itype(ires,j),j),j=1,5),ires,(c(j,ires),j=1,3),&
3941 (c(j,ires+nres),j=1,3)
3944 ! znamy już nres wiec mozna alokowac tablice
3945 ! Calculate internal coordinates.
3946 if(me.eq.king.or..not.out1file)then
3947 write (iout,'(a)') &
3948 "Backbone and SC coordinates as read from the PDB"
3950 write (iout,'(i5,i3,2x,a,3f8.3,5x,3f8.3)') &
3951 ires,itype(ires,1),restyp(itype(ires,1),1),(c(j,ires),j=1,3),&
3952 (c(j,nres+ires),j=1,3)
3955 ! NOW LETS ROCK! SORTING
3956 allocate(c_temporary(3,2*nres))
3957 allocate(itype_temporary(nres,5))
3958 if (.not.allocated(molnum)) allocate(molnum(nres+1))
3959 if (.not.allocated(istype)) write(iout,*) &
3960 "SOMETHING WRONG WITH ISTYTPE"
3961 allocate(istype_temp(nres))
3962 itype_temporary(:,:)=0
3966 if (itype(i,k).ne.0) then
3968 c_temporary(j,seqalingbegin)=c(j,i)
3969 c_temporary(j,seqalingbegin+nres)=c(j,i+nres)
3972 itype_temporary(seqalingbegin,k)=itype(i,k)
3973 print *,i,k,itype(i,k),itype_temporary(seqalingbegin,k),seqalingbegin
3974 istype_temp(seqalingbegin)=istype(i)
3975 molnum(seqalingbegin)=k
3976 seqalingbegin=seqalingbegin+1
3982 c(j,i)=c_temporary(j,i)
3987 itype(i,k)=itype_temporary(i,k)
3988 istype(i)=istype_temp(i)
3991 ! if (itype(1,1).eq.ntyp1) then
3994 ! if (unres_pdb) then
3995 ! 2/15/2013 by Adam: corrected insertion of the first dummy residue
3996 ! call refsys(2,3,4,e1,e2,e3,fail)
4003 ! c(j,1)=c(j,2)-1.9d0*e2(j)
4007 ! dcj=(c(j,4)-c(j,3))/2.0
4009 ! c(j,nres+1)=c(j,1)
4015 write (iout,'(/a)') &
4016 "Cartesian coordinates of the reference structure after sorting"
4017 write (iout,'(a,16x,3(3x,a5),5x,3(3x,a5))') &
4018 "Residue","X(CA)","Y(CA)","Z(CA)","X(SC)","Y(SC)","Z(SC)"
4020 write (iout,'(5(a3,1x),i5,3f8.3,5x,3f8.3)') &
4021 (restyp(itype(ires,j),j),j=1,5),ires,(c(j,ires),j=1,3),&
4022 (c(j,ires+nres),j=1,3)
4026 ! print *,seqalingbegin,nres
4027 if(.not.allocated(vbld)) then
4028 allocate(vbld(2*nres))
4033 if(.not.allocated(vbld_inv)) then
4034 allocate(vbld_inv(2*nres))
4040 if(.not.allocated(theta)) then
4041 allocate(theta(nres+2))
4045 if(.not.allocated(phi)) allocate(phi(nres+2))
4046 if(.not.allocated(alph)) allocate(alph(nres+2))
4047 if(.not.allocated(omeg)) allocate(omeg(nres+2))
4048 if(.not.allocated(thetaref)) allocate(thetaref(nres+2))
4049 if(.not.allocated(phiref)) allocate(phiref(nres+2))
4050 if(.not.allocated(costtab)) allocate(costtab(nres))
4051 if(.not.allocated(sinttab)) allocate(sinttab(nres))
4052 if(.not.allocated(cost2tab)) allocate(cost2tab(nres))
4053 if(.not.allocated(sint2tab)) allocate(sint2tab(nres))
4054 if(.not.allocated(xxref)) allocate(xxref(nres))
4055 if(.not.allocated(yyref)) allocate(yyref(nres))
4056 if(.not.allocated(zzref)) allocate(zzref(nres)) !(maxres)
4057 if(.not.allocated(dc_norm)) then
4058 ! if(.not.allocated(dc_norm)) allocate(dc_norm(3,0:2*nres+2))
4059 allocate(dc_norm(3,0:2*nres+2))
4063 call int_from_cart(.true.,.false.)
4064 call sc_loc_geom(.false.)
4066 thetaref(i)=theta(i)
4076 dc(j,i)=c(j,i+1)-c(j,i)
4077 dc_norm(j,i)=dc(j,i)*vbld_inv(i+1)
4082 dc(j,i+nres)=c(j,i+nres)-c(j,i)
4083 dc_norm(j,i+nres)=dc(j,i+nres)*vbld_inv(i+nres)
4085 ! write (iout,*) i,(dc(j,i+nres),j=1,3),(dc_norm(j,i+nres),j=1,3),&
4089 ! Copy the coordinates to reference coordinates
4090 ! Splits to single chain if occurs
4094 ! cref(j,i,cou)=c(j,i)
4098 if(.not.allocated(cref)) allocate(cref(3,2*nres+2,maxperm)) !(3,maxres2+2,maxperm)
4099 if(.not.allocated(chain_rep)) allocate(chain_rep(3,2*nres+2,maxsym)) !(3,maxres2+2,maxsym)
4100 if(.not.allocated(tabperm)) allocate(tabperm(maxperm,maxsym)) !(maxperm,maxsym)
4101 !-----------------------------
4105 write (iout,*) "symetr", symetr
4108 ! write (iout,*) "spraw lancuchy",(c(j,i),j=1,3)
4110 if ((itype(i-1,1).eq.ntyp1).and.(i.gt.2)) then
4113 ! write (iout,*) "spraw lancuchy",(c(j,i),j=1,3)
4118 cref(j,i,cou)=c(j,i)
4119 cref(j,i+nres,cou)=c(j,i+nres)
4121 chain_rep(j,lll,kkk)=c(j,i)
4122 chain_rep(j,lll+nres,kkk)=c(j,i+nres)
4126 write (iout,*) chain_length
4127 if (chain_length.eq.0) chain_length=nres
4129 chain_rep(j,chain_length,symetr)=chain_rep(j,chain_length,1)
4130 chain_rep(j,chain_length+nres,symetr) &
4131 =chain_rep(j,chain_length+nres,1)
4134 ! write (iout,*) "spraw lancuchy",chain_length,symetr
4136 ! do kkk=1,chain_length
4137 ! write (iout,*) itype(kkk,1),(chain_rep(j,kkk,i), j=1,3)
4141 ! makes copy of chains
4142 write (iout,*) "symetr", symetr
4147 if (symetr.gt.1) then
4154 write(iout,*) (tabperm(i,kkk),kkk=1,4)
4160 write (iout,*) i,icha
4161 do lll=1,chain_length
4163 if (cou.le.nres) then
4165 kupa=mod(lll,chain_length)
4166 iprzes=(kkk-1)*chain_length+lll
4167 if (kupa.eq.0) kupa=chain_length
4168 write (iout,*) "kupa", kupa
4169 cref(j,iprzes,i)=chain_rep(j,kupa,icha)
4170 cref(j,iprzes+nres,i)=chain_rep(j,kupa+nres,icha)
4177 !-koniec robienia kopii
4180 write (iout,*) "nowa struktura", nperm
4182 write (iout,110) restyp(itype(i,1),1),i,cref(1,i,kkk),&
4184 cref(3,i,kkk),cref(1,nres+i,kkk),&
4185 cref(2,nres+i,kkk),cref(3,nres+i,kkk)
4187 100 format (//' alpha-carbon coordinates ',&
4188 ' centroid coordinates'/ &
4189 ' ', 6X,'X',11X,'Y',11X,'Z', &
4190 10X,'X',11X,'Y',11X,'Z')
4191 110 format (a,'(',i5,')',6f12.5)
4197 bfrag(i,j)=bfrag(i,j)-ishift
4203 hfrag(i,j)=hfrag(i,j)-ishift
4209 end subroutine readpdb
4210 #if .not. defined(WHAM_RUN) && .not. defined(CLUSTER)
4211 !-----------------------------------------------------------------------------
4213 !-----------------------------------------------------------------------------
4214 subroutine read_control
4228 use random, only: random_init
4229 ! implicit real*8 (a-h,o-z)
4230 ! include 'DIMENSIONS'
4232 use prng, only:prng_restart
4234 logical :: OKRandom!, prng_restart
4237 ! include 'COMMON.IOUNITS'
4238 ! include 'COMMON.TIME1'
4239 ! include 'COMMON.THREAD'
4240 ! include 'COMMON.SBRIDGE'
4241 ! include 'COMMON.CONTROL'
4242 ! include 'COMMON.MCM'
4243 ! include 'COMMON.MAP'
4244 ! include 'COMMON.HEADER'
4245 ! include 'COMMON.CSA'
4246 ! include 'COMMON.CHAIN'
4247 ! include 'COMMON.MUCA'
4248 ! include 'COMMON.MD'
4249 ! include 'COMMON.FFIELD'
4250 ! include 'COMMON.INTERACT'
4251 ! include 'COMMON.SETUP'
4252 !el integer :: KDIAG,ICORFL,IXDR
4253 !el COMMON /MACHSW/ KDIAG,ICORFL,IXDR
4254 character(len=8),dimension(0:3) :: diagmeth = reshape((/'Library ',&
4255 'EVVRSP ','Givens ','Jacobi '/),shape(diagmeth))
4256 ! character(len=80) :: ucase
4257 character(len=640) :: controlcard
4259 real(kind=8) :: seed,rmsdbc,rmsdbc1max,rmsdbcm,drms,timem!,&
4265 read (INP,'(a)') titel
4266 call card_concat(controlcard,.true.)
4267 ! out1file=index(controlcard,'OUT1FILE').gt.0 .or. fg_rank.gt.0
4268 ! print *,"Processor",me," fg_rank",fg_rank," out1file",out1file
4269 call reada(controlcard,'SEED',seed,0.0D0)
4270 call random_init(seed)
4271 ! Set up the time limit (caution! The time must be input in minutes!)
4272 read_cart=index(controlcard,'READ_CART').gt.0
4273 call readi(controlcard,'CONSTR_DIST',constr_dist,0)
4274 call readi(controlcard,'SYM',symetr,1)
4275 call reada(controlcard,'TIMLIM',timlim,960.0D0) ! default 16 hours
4276 unres_pdb = index(controlcard,'UNRES_PDB') .gt. 0
4277 call reada(controlcard,'SAFETY',safety,30.0D0) ! default 30 minutes
4278 call reada(controlcard,'RMSDBC',rmsdbc,3.0D0)
4279 call reada(controlcard,'RMSDBC1',rmsdbc1,0.5D0)
4280 call reada(controlcard,'RMSDBC1MAX',rmsdbc1max,1.5D0)
4281 call reada(controlcard,'RMSDBCM',rmsdbcm,3.0D0)
4282 call reada(controlcard,'DRMS',drms,0.1D0)
4283 if(me.eq.king .or. .not. out1file .and. fg_rank.eq.0) then
4284 write (iout,'(a,f10.1)')'RMSDBC = ',rmsdbc
4285 write (iout,'(a,f10.1)')'RMSDBC1 = ',rmsdbc1
4286 write (iout,'(a,f10.1)')'RMSDBC1MAX = ',rmsdbc1max
4287 write (iout,'(a,f10.1)')'DRMS = ',drms
4288 write (iout,'(a,f10.1)')'RMSDBCM = ',rmsdbcm
4289 write (iout,'(a,f10.1)') 'Time limit (min):',timlim
4291 call readi(controlcard,'NZ_START',nz_start,0)
4292 call readi(controlcard,'NZ_END',nz_end,0)
4293 call readi(controlcard,'IZ_SC',iz_sc,0)
4294 timlim=60.0D0*timlim
4295 safety = 60.0d0*safety
4298 call reada(controlcard,"T_BATH",t_bath,300.0d0)
4299 !C SHIELD keyword sets if the shielding effect of side-chains is used
4300 !C 0 denots no shielding is used all peptide are equally despite the
4301 !C solvent accesible area
4302 !C 1 the newly introduced function
4303 !C 2 reseved for further possible developement
4304 call readi(controlcard,'SHIELD',shield_mode,0)
4305 !C if(me.eq.king .or. .not. out1file .and. fg_rank.eq.0) then
4306 write(iout,*) "shield_mode",shield_mode
4307 call readi(controlcard,'TORMODE',tor_mode,0)
4308 !C if(me.eq.king .or. .not. out1file .and. fg_rank.eq.0) then
4309 write(iout,*) "torsional and valence angle mode",tor_mode
4311 !C Varibles set size of box
4312 with_theta_constr = index(controlcard,"WITH_THETA_CONSTR").gt.0
4313 protein=index(controlcard,"PROTEIN").gt.0
4314 ions=index(controlcard,"IONS").gt.0
4315 call readi(controlcard,'OLDION',oldion,1)
4316 nucleic=index(controlcard,"NUCLEIC").gt.0
4317 write (iout,*) "with_theta_constr ",with_theta_constr
4318 AFMlog=(index(controlcard,'AFM'))
4319 selfguide=(index(controlcard,'SELFGUIDE'))
4320 print *,'AFMlog',AFMlog,selfguide,"KUPA"
4321 call readi(controlcard,'GENCONSTR',genconstr,0)
4322 call reada(controlcard,'BOXX',boxxsize,100.0d0)
4323 call reada(controlcard,'BOXY',boxysize,100.0d0)
4324 call reada(controlcard,'BOXZ',boxzsize,100.0d0)
4325 call readi(controlcard,'TUBEMOD',tubemode,0)
4326 print *,"SCELE",scelemode
4327 call readi(controlcard,"SCELEMODE",scelemode,0)
4328 print *,"SCELE",scelemode
4330 ! elemode = 0 is orignal UNRES electrostatics
4331 ! elemode = 1 is "Momo" potentials in progress
4332 ! elemode = 2 is in development EVALD
4335 write (iout,*) TUBEmode,"TUBEMODE"
4336 if (TUBEmode.gt.0) then
4337 call reada(controlcard,"XTUBE",tubecenter(1),0.0d0)
4338 call reada(controlcard,"YTUBE",tubecenter(2),0.0d0)
4339 call reada(controlcard,"ZTUBE",tubecenter(3),0.0d0)
4340 call reada(controlcard,"RTUBE",tubeR0,0.0d0)
4341 call reada(controlcard,"TUBETOP",bordtubetop,boxzsize)
4342 call reada(controlcard,"TUBEBOT",bordtubebot,0.0d0)
4343 call reada(controlcard,"TUBEBUF",tubebufthick,1.0d0)
4344 buftubebot=bordtubebot+tubebufthick
4345 buftubetop=bordtubetop-tubebufthick
4348 ! CUTOFFF ON ELECTROSTATICS
4349 call reada(controlcard,"R_CUT_ELE",r_cut_ele,15.0d0)
4350 call reada(controlcard,"LAMBDA_ELE",rlamb_ele,0.3d0)
4351 write(iout,*) "R_CUT_ELE=",r_cut_ele
4352 ! Lipidic parameters
4353 call reada(controlcard,"LIPTHICK",lipthick,0.0d0)
4354 call reada(controlcard,"LIPAQBUF",lipbufthick,0.0d0)
4355 if (lipthick.gt.0.0d0) then
4356 bordliptop=(boxzsize+lipthick)/2.0
4357 bordlipbot=bordliptop-lipthick
4358 if ((bordliptop.gt.boxzsize).or.(bordlipbot.lt.0.0)) &
4359 write(iout,*) "WARNING WRONG SIZE OF LIPIDIC PHASE"
4360 buflipbot=bordlipbot+lipbufthick
4361 bufliptop=bordliptop-lipbufthick
4362 if ((lipbufthick*2.0d0).gt.lipthick) &
4363 write(iout,*) "WARNING WRONG SIZE OF LIP AQ BUF"
4364 endif !lipthick.gt.0
4365 write(iout,*) "bordliptop=",bordliptop
4366 write(iout,*) "bordlipbot=",bordlipbot
4367 write(iout,*) "bufliptop=",bufliptop
4368 write(iout,*) "buflipbot=",buflipbot
4369 write (iout,*) "SHIELD MODE",shield_mode
4371 !C-------------------------
4372 minim=(index(controlcard,'MINIMIZE').gt.0)
4373 dccart=(index(controlcard,'CART').gt.0)
4374 overlapsc=(index(controlcard,'OVERLAP').gt.0)
4375 overlapsc=.not.overlapsc
4376 searchsc=(index(controlcard,'NOSEARCHSC').gt.0)
4377 searchsc=.not.searchsc
4378 sideadd=(index(controlcard,'SIDEADD').gt.0)
4379 energy_dec=(index(controlcard,'ENERGY_DEC').gt.0)
4380 outpdb=(index(controlcard,'PDBOUT').gt.0)
4381 outmol2=(index(controlcard,'MOL2OUT').gt.0)
4382 pdbref=(index(controlcard,'PDBREF').gt.0)
4383 refstr=pdbref .or. (index(controlcard,'REFSTR').gt.0)
4384 indpdb=index(controlcard,'PDBSTART')
4385 extconf=(index(controlcard,'EXTCONF').gt.0)
4386 call readi(controlcard,'IPRINT',iprint,0)
4387 call readi(controlcard,'MAXGEN',maxgen,10000)
4388 call readi(controlcard,'MAXOVERLAP',maxoverlap,1000)
4389 call readi(controlcard,"KDIAG",kdiag,0)
4390 call readi(controlcard,"RESCALE_MODE",rescale_mode,2)
4391 if(me.eq.king .or. .not. out1file .and. fg_rank.eq.0) &
4392 write (iout,*) "RESCALE_MODE",rescale_mode
4393 split_ene=index(controlcard,'SPLIT_ENE').gt.0
4394 if (index(controlcard,'REGULAR').gt.0.0D0) then
4395 call reada(controlcard,'WEIDIS',weidis,0.1D0)
4399 if (index(controlcard,'CHECKGRAD').gt.0) then
4401 if (index(controlcard,'CART').gt.0) then
4403 elseif (index(controlcard,'CARINT').gt.0) then
4408 elseif (index(controlcard,'THREAD').gt.0) then
4410 call readi(controlcard,'THREAD',nthread,0)
4411 if (nthread.gt.0) then
4412 call reada(controlcard,'WEIDIS',weidis,0.1D0)
4415 write (iout,'(a)')'A number has to follow the THREAD keyword.'
4416 stop 'Error termination in Read_Control.'
4418 else if (index(controlcard,'MCMA').gt.0) then
4420 else if (index(controlcard,'MCEE').gt.0) then
4422 else if (index(controlcard,'MULTCONF').gt.0) then
4424 else if (index(controlcard,'MAP').gt.0) then
4426 call readi(controlcard,'MAP',nmap,0)
4427 else if (index(controlcard,'CSA').gt.0) then
4429 !rc else if (index(controlcard,'ZSCORE').gt.0) then
4431 !rc ZSCORE is rm from UNRES, modecalc=9 is available
4434 !fcm else if (index(controlcard,'MCMF').gt.0) then
4436 else if (index(controlcard,'SOFTREG').gt.0) then
4438 else if (index(controlcard,'CHECK_BOND').gt.0) then
4440 else if (index(controlcard,'TEST').gt.0) then
4442 else if (index(controlcard,'MD').gt.0) then
4444 else if (index(controlcard,'RE ').gt.0) then
4448 lmuca=index(controlcard,'MUCA').gt.0
4449 call readi(controlcard,'MUCADYN',mucadyn,0)
4450 call readi(controlcard,'MUCASMOOTH',muca_smooth,0)
4451 if (lmuca .and. (me.eq.king .or. .not.out1file )) &
4453 write (iout,*) 'MUCADYN=',mucadyn
4454 write (iout,*) 'MUCASMOOTH=',muca_smooth
4457 iscode=index(controlcard,'ONE_LETTER')
4458 indphi=index(controlcard,'PHI')
4459 indback=index(controlcard,'BACK')
4460 iranconf=index(controlcard,'RAND_CONF')
4461 i2ndstr=index(controlcard,'USE_SEC_PRED')
4462 gradout=index(controlcard,'GRADOUT').gt.0
4463 gnorm_check=index(controlcard,'GNORM_CHECK').gt.0
4464 call reada(controlcard,'DISTCHAINMAX',distchainmax,5.0d0)
4465 if (me.eq.king .or. .not.out1file ) &
4466 write (iout,*) "DISTCHAINMAX",distchainmax
4468 if(me.eq.king.or..not.out1file) &
4469 write (iout,'(2a)') diagmeth(kdiag),&
4470 ' routine used to diagonalize matrices.'
4471 if (shield_mode.gt.0) then
4472 pi=4.0D0*datan(1.0D0)
4473 !C VSolvSphere the volume of solving sphere
4475 !C rpp(1,1) is the energy r0 for peptide group contact and will be used for it
4476 !C there will be no distinction between proline peptide group and normal peptide
4477 !C group in case of shielding parameters
4478 VSolvSphere=4.0/3.0*pi*(4.50d0)**3
4479 VSolvSphere_div=VSolvSphere-4.0/3.0*pi*(4.50/2.0)**3
4480 write (iout,*) VSolvSphere,VSolvSphere_div
4481 !C long axis of side chain
4483 ! long_r_sidechain(i)=vbldsc0(1,i)
4484 ! short_r_sidechain(i)=sigma0(i)
4485 ! write(iout,*) "parame for long and short axis",i,vbldsc0(1,i),&
4491 end subroutine read_control
4492 !-----------------------------------------------------------------------------
4493 subroutine read_REMDpar
4495 ! Read REMD settings
4502 use control_data, only:out1file
4503 ! implicit real*8 (a-h,o-z)
4504 ! include 'DIMENSIONS'
4505 ! include 'COMMON.IOUNITS'
4506 ! include 'COMMON.TIME1'
4507 ! include 'COMMON.MD'
4510 !el include 'COMMON.LANGEVIN'
4512 !el include 'COMMON.LANGEVIN.lang0'
4514 ! include 'COMMON.INTERACT'
4515 ! include 'COMMON.NAMES'
4516 ! include 'COMMON.GEO'
4517 ! include 'COMMON.REMD'
4518 ! include 'COMMON.CONTROL'
4519 ! include 'COMMON.SETUP'
4520 ! character(len=80) :: ucase
4521 character(len=320) :: controlcard
4522 character(len=3200) :: controlcard1
4523 integer :: iremd_m_total
4526 ! real(kind=8) :: var,ene
4528 if(me.eq.king.or..not.out1file) &
4529 write (iout,*) "REMD setup"
4531 call card_concat(controlcard,.true.)
4532 call readi(controlcard,"NREP",nrep,3)
4533 call readi(controlcard,"NSTEX",nstex,1000)
4534 call reada(controlcard,"RETMIN",retmin,10.0d0)
4535 call reada(controlcard,"RETMAX",retmax,1000.0d0)
4536 mremdsync=(index(controlcard,'SYNC').gt.0)
4537 call readi(controlcard,"NSYN",i_sync_step,100)
4538 restart1file=(index(controlcard,'REST1FILE').gt.0)
4539 traj1file=(index(controlcard,'TRAJ1FILE').gt.0)
4540 call readi(controlcard,"TRAJCACHE",max_cache_traj_use,1)
4541 if(max_cache_traj_use.gt.max_cache_traj) &
4542 max_cache_traj_use=max_cache_traj
4543 if(me.eq.king.or..not.out1file) then
4544 !d if (traj1file) then
4545 !rc caching is in testing - NTWX is not ignored
4546 !d write (iout,*) "NTWX value is ignored"
4547 !d write (iout,*) " trajectory is stored to one file by master"
4548 !d write (iout,*) " before exchange at NSTEX intervals"
4550 write (iout,*) "NREP= ",nrep
4551 write (iout,*) "NSTEX= ",nstex
4552 write (iout,*) "SYNC= ",mremdsync
4553 write (iout,*) "NSYN= ",i_sync_step
4554 write (iout,*) "TRAJCACHE= ",max_cache_traj_use
4557 allocate(remd_t(nrep),remd_m(nrep)) !(maxprocs)
4558 if (index(controlcard,'TLIST').gt.0) then
4560 call card_concat(controlcard1,.true.)
4561 read(controlcard1,*) (remd_t(i),i=1,nrep)
4562 if(me.eq.king.or..not.out1file) &
4563 write (iout,*)'tlist',(remd_t(i),i=1,nrep)
4566 if (index(controlcard,'MLIST').gt.0) then
4568 call card_concat(controlcard1,.true.)
4569 read(controlcard1,*) (remd_m(i),i=1,nrep)
4570 if(me.eq.king.or..not.out1file) then
4571 write (iout,*)'mlist',(remd_m(i),i=1,nrep)
4574 iremd_m_total=iremd_m_total+remd_m(i)
4576 write (iout,*) 'Total number of replicas ',iremd_m_total
4579 if(me.eq.king.or..not.out1file) &
4580 write (iout,'(/30(1h=),a,29(1h=)/)') " End of REMD run setup "
4582 end subroutine read_REMDpar
4583 !-----------------------------------------------------------------------------
4584 subroutine read_MDpar
4588 use control_data, only: r_cut,rlamb,out1file
4590 use geometry_data, only: pi
4592 ! implicit real*8 (a-h,o-z)
4593 ! include 'DIMENSIONS'
4594 ! include 'COMMON.IOUNITS'
4595 ! include 'COMMON.TIME1'
4596 ! include 'COMMON.MD'
4599 !el include 'COMMON.LANGEVIN'
4601 !el include 'COMMON.LANGEVIN.lang0'
4603 ! include 'COMMON.INTERACT'
4604 ! include 'COMMON.NAMES'
4605 ! include 'COMMON.GEO'
4606 ! include 'COMMON.SETUP'
4607 ! include 'COMMON.CONTROL'
4608 ! include 'COMMON.SPLITELE'
4609 ! character(len=80) :: ucase
4610 character(len=320) :: controlcard
4615 call card_concat(controlcard,.true.)
4616 call readi(controlcard,"NSTEP",n_timestep,1000000)
4617 call readi(controlcard,"NTWE",ntwe,100)
4618 call readi(controlcard,"NTWX",ntwx,1000)
4619 call reada(controlcard,"DT",d_time,1.0d-1)
4620 call reada(controlcard,"DVMAX",dvmax,2.0d1)
4621 call reada(controlcard,"DAMAX",damax,1.0d1)
4622 call reada(controlcard,"EDRIFTMAX",edriftmax,1.0d+1)
4623 call readi(controlcard,"LANG",lang,0)
4624 RESPA = index(controlcard,"RESPA") .gt. 0
4625 call readi(controlcard,"NTIME_SPLIT",ntime_split,1)
4626 ntime_split0=ntime_split
4627 call readi(controlcard,"MAXTIME_SPLIT",maxtime_split,64)
4628 ntime_split0=ntime_split
4629 call reada(controlcard,"R_CUT",r_cut,2.0d0)
4630 call reada(controlcard,"LAMBDA",rlamb,0.3d0)
4631 rest = index(controlcard,"REST").gt.0
4632 tbf = index(controlcard,"TBF").gt.0
4633 usampl = index(controlcard,"USAMPL").gt.0
4634 mdpdb = index(controlcard,"MDPDB").gt.0
4635 call reada(controlcard,"T_BATH",t_bath,300.0d0)
4636 call reada(controlcard,"TAU_BATH",tau_bath,1.0d-1)
4637 call reada(controlcard,"EQ_TIME",eq_time,1.0d+4)
4638 call readi(controlcard,"RESET_MOMENT",count_reset_moment,1000)
4639 if (count_reset_moment.eq.0) count_reset_moment=1000000000
4640 call readi(controlcard,"RESET_VEL",count_reset_vel,1000)
4641 reset_moment=lang.eq.0 .and. tbf .and. count_reset_moment.gt.0
4642 reset_vel=lang.eq.0 .and. tbf .and. count_reset_vel.gt.0
4643 if (count_reset_vel.eq.0) count_reset_vel=1000000000
4644 large = index(controlcard,"LARGE").gt.0
4645 print_compon = index(controlcard,"PRINT_COMPON").gt.0
4646 rattle = index(controlcard,"RATTLE").gt.0
4647 preminim=(index(controlcard,'PREMINIM').gt.0)
4648 write (iout,*) "PREMINIM ",preminim
4649 dccart=(index(controlcard,'CART').gt.0)
4650 if (preminim) call read_minim
4651 ! if performing umbrella sampling, fragments constrained are read from the fragment file
4657 if(me.eq.king.or..not.out1file) then
4659 write (iout,'(27(1h=),a26,27(1h=))') " Parameters of the MD run "
4661 write (iout,'(a)') "The units are:"
4662 write (iout,'(a)') "positions: angstrom, time: 48.9 fs"
4663 write (iout,'(2a)') "velocity: angstrom/(48.9 fs),",&
4664 " acceleration: angstrom/(48.9 fs)**2"
4665 write (iout,'(a)') "energy: kcal/mol, temperature: K"
4667 write (iout,'(a60,i10)') "Number of time steps:",n_timestep
4668 write (iout,'(a60,f10.5,a)') &
4669 "Initial time step of numerical integration:",d_time,&
4671 write (iout,'(60x,f10.5,a)') d_time*48.9," fs"
4673 write (iout,'(2a,i4,a)') &
4674 "A-MTS algorithm used; initial time step for fast-varying",&
4675 " short-range forces split into",ntime_split," steps."
4676 write (iout,'(a,f5.2,a,f5.2)') "Short-range force cutoff",&
4677 r_cut," lambda",rlamb
4679 write (iout,'(2a,f10.5)') &
4680 "Maximum acceleration threshold to reduce the time step",&
4681 "/increase split number:",damax
4682 write (iout,'(2a,f10.5)') &
4683 "Maximum predicted energy drift to reduce the timestep",&
4684 "/increase split number:",edriftmax
4685 write (iout,'(a60,f10.5)') &
4686 "Maximum velocity threshold to reduce velocities:",dvmax
4687 write (iout,'(a60,i10)') "Frequency of property output:",ntwe
4688 write (iout,'(a60,i10)') "Frequency of coordinate output:",ntwx
4689 if (rattle) write (iout,'(a60)') &
4690 "Rattle algorithm used to constrain the virtual bonds"
4694 call reada(controlcard,"ETAWAT",etawat,0.8904d0)
4695 call reada(controlcard,"RWAT",rwat,1.4d0)
4696 call reada(controlcard,"SCAL_FRIC",scal_fric,2.0d-2)
4697 surfarea=index(controlcard,"SURFAREA").gt.0
4698 call readi(controlcard,"RESET_FRICMAT",reset_fricmat,1000)
4699 if(me.eq.king.or..not.out1file)then
4700 write (iout,'(/a,$)') "Langevin dynamics calculation"
4702 write (iout,'(a/)') &
4703 " with direct integration of Langevin equations"
4704 else if (lang.eq.2) then
4705 write (iout,'(a/)') " with TINKER stochasic MD integrator"
4706 else if (lang.eq.3) then
4707 write (iout,'(a/)') " with Ciccotti's stochasic MD integrator"
4708 else if (lang.eq.4) then
4709 write (iout,'(a/)') " in overdamped mode"
4711 write (iout,'(//a,i5)') &
4712 "=========== ERROR: Unknown Langevin dynamics mode:",lang
4715 write (iout,'(a60,f10.5)') "Temperature:",t_bath
4716 write (iout,'(a60,f10.5)') "Viscosity of the solvent:",etawat
4717 write (iout,'(a60,f10.5)') "Radius of solvent molecule:",rwat
4718 write (iout,'(a60,f10.5)') &
4719 "Scaling factor of the friction forces:",scal_fric
4720 if (surfarea) write (iout,'(2a,i10,a)') &
4721 "Friction coefficients will be scaled by solvent-accessible",&
4722 " surface area every",reset_fricmat," steps."
4724 ! Calculate friction coefficients and bounds of stochastic forces
4725 eta=6*pi*cPoise*etawat
4726 if(me.eq.king.or..not.out1file) &
4727 write(iout,'(a60,f10.5)')"Eta of the solvent in natural units:",&
4730 do j=1,5 !types of molecules
4731 gamp(j)=scal_fric*(pstok(j)+rwat)*eta
4732 stdfp(j)=dsqrt(2*Rb*t_bath/d_time)
4734 allocate(gamsc(ntyp1,5),stdfsc(ntyp1,5)) !(ntyp1)
4735 do j=1,5 !types of molecules
4737 gamsc(i,j)=scal_fric*(restok(i,j)+rwat)*eta
4738 stdfsc(i,j)=dsqrt(2*Rb*t_bath/d_time)
4742 if(me.eq.king.or..not.out1file)then
4743 write (iout,'(/2a/)') &
4744 "Radii of site types and friction coefficients and std's of",&
4745 " stochastic forces of fully exposed sites"
4746 write (iout,'(a5,f5.2,2f10.5)')'p',pstok,gamp(1),stdfp*dsqrt(gamp(1))
4748 write (iout,'(a5,f5.2,2f10.5)') restyp(i,1),restok(i,1),&
4749 gamsc(i,1),stdfsc(i,1)*dsqrt(gamsc(i,1))
4753 if(me.eq.king.or..not.out1file)then
4754 write (iout,'(a)') "Berendsen bath calculation"
4755 write (iout,'(a60,f10.5)') "Temperature:",t_bath
4756 write (iout,'(a60,f10.5)') "Coupling constant (tau):",tau_bath
4758 write (iout,'(a,i10,a)') "Momenta will be reset at zero every",&
4759 count_reset_moment," steps"
4761 write (iout,'(a,i10,a)') &
4762 "Velocities will be reset at random every",count_reset_vel,&
4766 if(me.eq.king.or..not.out1file) &
4767 write (iout,'(a31)') "Microcanonical mode calculation"
4769 if(me.eq.king.or..not.out1file)then
4770 if (rest) write (iout,'(/a/)') "===== Calculation restarted ===="
4772 write(iout,*) "MD running with constraints."
4773 write(iout,*) "Equilibration time ", eq_time, " mtus."
4774 write(iout,*) "Constraining ", nfrag," fragments."
4775 write(iout,*) "Length of each fragment, weight and q0:"
4777 write (iout,*) "Set of restraints #",iset
4779 write(iout,'(2i5,f8.1,f7.4)') ifrag(1,i,iset),&
4780 ifrag(2,i,iset),wfrag(i,iset),qinfrag(i,iset)
4782 write(iout,*) "constraints between ", npair, "fragments."
4783 write(iout,*) "constraint pairs, weights and q0:"
4785 write(iout,'(2i5,f8.1,f7.4)') ipair(1,i,iset),&
4786 ipair(2,i,iset),wpair(i,iset),qinpair(i,iset)
4788 write(iout,*) "angle constraints within ", nfrag_back,&
4789 "backbone fragments."
4790 write(iout,*) "fragment, weights:"
4792 write(iout,'(2i5,3f8.1)') ifrag_back(1,i,iset),&
4793 ifrag_back(2,i,iset),wfrag_back(1,i,iset),&
4794 wfrag_back(2,i,iset),wfrag_back(3,i,iset)
4797 iset=mod(kolor,nset)+1
4800 if(me.eq.king.or..not.out1file) &
4801 write (iout,'(/30(1h=),a,29(1h=)/)') " End of MD run setup "
4803 end subroutine read_MDpar
4804 !-----------------------------------------------------------------------------
4808 ! implicit real*8 (a-h,o-z)
4809 ! include 'DIMENSIONS'
4810 ! include 'COMMON.MAP'
4811 ! include 'COMMON.IOUNITS'
4812 character(len=3) :: angid(4) = (/'THE','PHI','ALP','OME'/)
4813 character(len=80) :: mapcard !,ucase
4816 ! real(kind=8) :: var,ene
4819 read (inp,'(a)') mapcard
4820 mapcard=ucase(mapcard)
4821 if (index(mapcard,'PHI').gt.0) then
4823 else if (index(mapcard,'THE').gt.0) then
4825 else if (index(mapcard,'ALP').gt.0) then
4827 else if (index(mapcard,'OME').gt.0) then
4830 write(iout,'(a)')'Error - illegal variable spec in MAP card.'
4831 stop 'Error - illegal variable spec in MAP card.'
4833 call readi (mapcard,'RES1',res1(imap),0)
4834 call readi (mapcard,'RES2',res2(imap),0)
4835 if (res1(imap).eq.0) then
4836 res1(imap)=res2(imap)
4837 else if (res2(imap).eq.0) then
4838 res2(imap)=res1(imap)
4840 if(res1(imap)*res2(imap).eq.0 .or. res1(imap).gt.res2(imap))then
4841 write (iout,'(a)') &
4842 'Error - illegal definition of variable group in MAP.'
4843 stop 'Error - illegal definition of variable group in MAP.'
4845 call reada(mapcard,'FROM',ang_from(imap),0.0D0)
4846 call reada(mapcard,'TO',ang_to(imap),0.0D0)
4847 call readi(mapcard,'NSTEP',nstep(imap),0)
4848 if (ang_from(imap).eq.ang_to(imap) .or. nstep(imap).eq.0) then
4849 write (iout,'(a)') &
4850 'Illegal boundary and/or step size specification in MAP.'
4851 stop 'Illegal boundary and/or step size specification in MAP.'
4855 end subroutine map_read
4856 !-----------------------------------------------------------------------------
4859 use control_data, only: vdisulf
4861 ! implicit real*8 (a-h,o-z)
4862 ! include 'DIMENSIONS'
4863 ! include 'COMMON.IOUNITS'
4864 ! include 'COMMON.GEO'
4865 ! include 'COMMON.CSA'
4866 ! include 'COMMON.BANK'
4867 ! include 'COMMON.CONTROL'
4868 ! character(len=80) :: ucase
4869 character(len=620) :: mcmcard
4871 ! integer :: ntf,ik,iw_pdb
4872 ! real(kind=8) :: var,ene
4874 call card_concat(mcmcard,.true.)
4876 call readi(mcmcard,'NCONF',nconf,50)
4877 call readi(mcmcard,'NADD',nadd,0)
4878 call readi(mcmcard,'JSTART',jstart,1)
4879 call readi(mcmcard,'JEND',jend,1)
4880 call readi(mcmcard,'NSTMAX',nstmax,500000)
4881 call readi(mcmcard,'N0',n0,1)
4882 call readi(mcmcard,'N1',n1,6)
4883 call readi(mcmcard,'N2',n2,4)
4884 call readi(mcmcard,'N3',n3,0)
4885 call readi(mcmcard,'N4',n4,0)
4886 call readi(mcmcard,'N5',n5,0)
4887 call readi(mcmcard,'N6',n6,10)
4888 call readi(mcmcard,'N7',n7,0)
4889 call readi(mcmcard,'N8',n8,0)
4890 call readi(mcmcard,'N9',n9,0)
4891 call readi(mcmcard,'N14',n14,0)
4892 call readi(mcmcard,'N15',n15,0)
4893 call readi(mcmcard,'N16',n16,0)
4894 call readi(mcmcard,'N17',n17,0)
4895 call readi(mcmcard,'N18',n18,0)
4897 vdisulf=(index(mcmcard,'DYNSS').gt.0)
4899 call readi(mcmcard,'NDIFF',ndiff,2)
4900 call reada(mcmcard,'DIFFCUT',diffcut,0.0d0)
4901 call readi(mcmcard,'IS1',is1,1)
4902 call readi(mcmcard,'IS2',is2,8)
4903 call readi(mcmcard,'NRAN0',nran0,4)
4904 call readi(mcmcard,'NRAN1',nran1,2)
4905 call readi(mcmcard,'IRR',irr,1)
4906 call readi(mcmcard,'NSEED',nseed,20)
4907 call readi(mcmcard,'NTOTAL',ntotal,10000)
4908 call reada(mcmcard,'CUT1',cut1,2.0d0)
4909 call reada(mcmcard,'CUT2',cut2,5.0d0)
4910 call reada(mcmcard,'ESTOP',estop,-3000.0d0)
4911 call readi(mcmcard,'ICMAX',icmax,3)
4912 call readi(mcmcard,'IRESTART',irestart,0)
4913 !!bankt call readi(mcmcard,'NBANKTM',ntbankm,0)
4916 call reada(mcmcard,'DELE',dele,20.0d0)
4917 call reada(mcmcard,'DIFCUT',difcut,720.0d0)
4918 call readi(mcmcard,'IREF',iref,0)
4919 call reada(mcmcard,'RMSCUT',rmscut,4.0d0)
4920 call reada(mcmcard,'PNCCUT',pnccut,0.5d0)
4921 call readi(mcmcard,'NCONF_IN',nconf_in,0)
4922 call reada(mcmcard,'RDIH_BIAS',rdih_bias,0.5d0)
4923 write (iout,*) "NCONF_IN",nconf_in
4925 end subroutine csaread
4926 !-----------------------------------------------------------------------------
4930 use control_data, only: MaxMoveType
4933 ! implicit real*8 (a-h,o-z)
4934 ! include 'DIMENSIONS'
4935 ! include 'COMMON.MCM'
4936 ! include 'COMMON.MCE'
4937 ! include 'COMMON.IOUNITS'
4938 ! character(len=80) :: ucase
4939 character(len=320) :: mcmcard
4942 ! real(kind=8) :: var,ene
4944 call card_concat(mcmcard,.true.)
4945 call readi(mcmcard,'MAXACC',maxacc,100)
4946 call readi(mcmcard,'MAX_MCM_IT',max_mcm_it,10000)
4947 call readi(mcmcard,'MAXTRIAL',maxtrial,100)
4948 call readi(mcmcard,'MAXTRIAL_ITER',maxtrial_iter,1000)
4949 call readi(mcmcard,'MAXREPM',maxrepm,200)
4950 call reada(mcmcard,'RANFRACT',RanFract,0.5D0)
4951 call reada(mcmcard,'POOL_FRACT',pool_fraction,0.01D0)
4952 call reada(mcmcard,'OVERLAP',overlap_cut,1.0D3)
4953 call reada(mcmcard,'E_UP',e_up,5.0D0)
4954 call reada(mcmcard,'DELTE',delte,0.1D0)
4955 call readi(mcmcard,'NSWEEP',nsweep,5)
4956 call readi(mcmcard,'NSTEPH',nsteph,0)
4957 call readi(mcmcard,'NSTEPC',nstepc,0)
4958 call reada(mcmcard,'TMIN',tmin,298.0D0)
4959 call reada(mcmcard,'TMAX',tmax,298.0D0)
4960 call readi(mcmcard,'NWINDOW',nwindow,0)
4961 call readi(mcmcard,'PRINT_MC',print_mc,0)
4962 print_stat=(index(mcmcard,'NO_PRINT_STAT').le.0)
4963 print_int=(index(mcmcard,'NO_PRINT_INT').le.0)
4964 ent_read=(index(mcmcard,'ENT_READ').gt.0)
4965 call readi(mcmcard,'SAVE_FREQ',save_frequency,1000)
4966 call readi(mcmcard,'MESSAGE_FREQ',message_frequency,1000)
4967 call readi(mcmcard,'POOL_READ_FREQ',pool_read_freq,5000)
4968 call readi(mcmcard,'POOL_SAVE_FREQ',pool_save_freq,1000)
4969 call readi(mcmcard,'PRINT_FREQ',print_freq,1000)
4970 if (nwindow.gt.0) then
4971 allocate(winstart(nwindow)) !!el (maxres)
4972 allocate(winend(nwindow)) !!el
4973 allocate(winlen(nwindow)) !!el
4974 read (inp,*) (winstart(i),winend(i),i=1,nwindow)
4976 winlen(i)=winend(i)-winstart(i)+1
4979 if (tmax.lt.tmin) tmax=tmin
4980 if (tmax.eq.tmin) then
4984 if (nstepc.gt.0 .and. nsteph.gt.0) then
4985 tsteph=(tmax/tmin)**(1.0D0/(nsteph+0.0D0))
4986 tstepc=(tmax/tmin)**(1.0D0/(nstepc+0.0D0))
4988 allocate(sumpro_type(0:MaxMoveType)) !(0:MaxMoveType)
4989 ! Probabilities of different move types
4990 sumpro_type(0)=0.0D0
4991 call reada(mcmcard,'MULTI_BOND',sumpro_type(1),1.0d0)
4992 call reada(mcmcard,'ONE_ANGLE' ,sumpro_type(2),2.0d0)
4993 sumpro_type(2)=sumpro_type(1)+sumpro_type(2)
4994 call reada(mcmcard,'THETA' ,sumpro_type(3),0.0d0)
4995 sumpro_type(3)=sumpro_type(2)+sumpro_type(3)
4996 call reada(mcmcard,'SIDE_CHAIN',sumpro_type(4),0.5d0)
4997 sumpro_type(4)=sumpro_type(3)+sumpro_type(4)
4999 print *,'i',i,' sumprotype',sumpro_type(i)
5000 sumpro_type(i)=sumpro_type(i)/sumpro_type(MaxMoveType)
5001 print *,'i',i,' sumprotype',sumpro_type(i)
5004 end subroutine mcmread
5005 !-----------------------------------------------------------------------------
5006 subroutine read_minim
5009 ! implicit real*8 (a-h,o-z)
5010 ! include 'DIMENSIONS'
5011 ! include 'COMMON.MINIM'
5012 ! include 'COMMON.IOUNITS'
5013 ! character(len=80) :: ucase
5014 character(len=320) :: minimcard
5016 ! integer :: ntf,ik,iw_pdb
5017 ! real(kind=8) :: var,ene
5019 call card_concat(minimcard,.true.)
5020 call readi(minimcard,'MAXMIN',maxmin,2000)
5021 call readi(minimcard,'MAXFUN',maxfun,5000)
5022 call readi(minimcard,'MINMIN',minmin,maxmin)
5023 call readi(minimcard,'MINFUN',minfun,maxmin)
5024 call reada(minimcard,'TOLF',tolf,1.0D-2)
5025 call reada(minimcard,'RTOLF',rtolf,1.0D-4)
5026 print_min_stat=min0(index(minimcard,'PRINT_MIN_STAT'),1)
5027 print_min_res=min0(index(minimcard,'PRINT_MIN_RES'),1)
5028 print_min_ini=min0(index(minimcard,'PRINT_MIN_INI'),1)
5029 write (iout,'(/80(1h*)/20x,a/80(1h*))') &
5030 'Options in energy minimization:'
5031 write (iout,'(4(a,i5),a,1pe14.5,a,1pe14.5)') &
5032 'MaxMin:',MaxMin,' MaxFun:',MaxFun,&
5033 'MinMin:',MinMin,' MinFun:',MinFun,&
5034 ' TolF:',TolF,' RTolF:',RTolF
5036 end subroutine read_minim
5037 !-----------------------------------------------------------------------------
5038 subroutine openunits
5040 use MD_data, only: usampl
5043 use control_data, only:out1file
5044 use control, only: getenv_loc
5045 ! implicit real*8 (a-h,o-z)
5046 ! include 'DIMENSIONS'
5049 character(len=16) :: form,nodename
5050 integer :: nodelen,ierror,npos
5052 ! include 'COMMON.SETUP'
5053 ! include 'COMMON.IOUNITS'
5054 ! include 'COMMON.MD'
5055 ! include 'COMMON.CONTROL'
5056 integer :: lenpre,lenpot,lentmp !,ilen
5058 character(len=3) :: out1file_text !,ucase
5059 character(len=3) :: ll
5062 ! integer :: ntf,ik,iw_pdb
5063 ! real(kind=8) :: var,ene
5065 ! print *,"Processor",myrank,"fg_rank",fg_rank," entered openunits"
5066 call getenv_loc("PREFIX",prefix)
5068 call getenv_loc("POT",pot)
5069 call getenv_loc("DIRTMP",tmpdir)
5070 call getenv_loc("CURDIR",curdir)
5071 call getenv_loc("OUT1FILE",out1file_text)
5072 ! print *,"Processor",myrank,"fg_rank",fg_rank," did GETENV"
5073 out1file_text=ucase(out1file_text)
5074 if (out1file_text(1:1).eq."Y") then
5077 out1file=fg_rank.gt.0
5082 if (lentmp.gt.0) then
5083 write (*,'(80(1h!))')
5084 write (*,'(a,19x,a,19x,a)') "!"," A T T E N T I O N ","!"
5085 write (*,'(80(1h!))')
5086 write (*,*)"All output files will be on node /tmp directory."
5088 call MPI_GET_PROCESSOR_NAME( nodename, nodelen, IERROR )
5089 if (me.eq.king) then
5090 write (*,*) "The master node is ",nodename
5091 else if (fg_rank.eq.0) then
5092 write (*,*) "I am the CG slave node ",nodename
5094 write (*,*) "I am the FG slave node ",nodename
5097 PREFIX = tmpdir(:lentmp)//'/'//prefix(:lenpre)
5098 lenpre = lentmp+lenpre+1
5100 entname=prefix(:lenpre)//'_'//pot(:lenpot)//'.entr'
5101 ! Get the names and open the input files
5102 #if defined(WINIFL) || defined(WINPGI)
5103 open(1,file=pref_orig(:ilen(pref_orig))// &
5104 '.inp',status='old',readonly,shared)
5105 open (9,file=prefix(:ilen(prefix))//'.intin',status='unknown')
5106 ! open (18,file=prefix(:ilen(prefix))//'.entin',status='unknown')
5107 ! Get parameter filenames and open the parameter files.
5108 call getenv_loc('BONDPAR',bondname)
5109 open (ibond,file=bondname,status='old',readonly,shared)
5110 call getenv_loc('BONDPAR_NUCL',bondname_nucl)
5111 open (ibond_nucl,file=bondname_nucl,status='old',readonly,shared)
5112 call getenv_loc('THETPAR',thetname)
5113 open (ithep,file=thetname,status='old',readonly,shared)
5114 call getenv_loc('ROTPAR',rotname)
5115 open (irotam,file=rotname,status='old',readonly,shared)
5116 call getenv_loc('TORPAR',torname)
5117 open (itorp,file=torname,status='old',readonly,shared)
5118 call getenv_loc('TORDPAR',tordname)
5119 open (itordp,file=tordname,status='old',readonly,shared)
5120 call getenv_loc('FOURIER',fouriername)
5121 open (ifourier,file=fouriername,status='old',readonly,shared)
5122 call getenv_loc('ELEPAR',elename)
5123 open (ielep,file=elename,status='old',readonly,shared)
5124 call getenv_loc('SIDEPAR',sidename)
5125 open (isidep,file=sidename,status='old',readonly,shared)
5127 call getenv_loc('THETPAR_NUCL',thetname_nucl)
5128 open (ithep_nucl,file=thetname_nucl,status='old',readonly,shared)
5129 call getenv_loc('ROTPAR_NUCL',rotname_nucl)
5130 open (irotam_nucl,file=rotname_nucl,status='old',readonly,shared)
5131 call getenv_loc('TORPAR_NUCL',torname_nucl)
5132 open (itorp_nucl,file=torname_nucl,status='old',readonly,shared)
5133 call getenv_loc('TORDPAR_NUCL',tordname_nucl)
5134 open (itordp_nucl,file=tordname_nucl,status='old',readonly,shared)
5135 call getenv_loc('SIDEPAR_NUCL',sidename_nucl)
5136 open (isidep_nucl,file=sidename_nucl,status='old',readonly,shared)
5139 #elif (defined CRAY) || (defined AIX)
5140 open(1,file=pref_orig(:ilen(pref_orig))//'.inp',status='old',&
5142 ! print *,"Processor",myrank," opened file 1"
5143 open (9,file=prefix(:ilen(prefix))//'.intin',status='unknown')
5144 ! print *,"Processor",myrank," opened file 9"
5145 ! open (18,file=prefix(:ilen(prefix))//'.entin',status='unknown')
5146 ! Get parameter filenames and open the parameter files.
5147 call getenv_loc('BONDPAR',bondname)
5148 open (ibond,file=bondname,status='old',action='read')
5149 call getenv_loc('BONDPAR_NUCL',bondname_nucl)
5150 open (ibond_nucl,file=bondname_nucl,status='old',action='read')
5152 ! print *,"Processor",myrank," opened file IBOND"
5153 call getenv_loc('THETPAR',thetname)
5154 open (ithep,file=thetname,status='old',action='read')
5155 ! print *,"Processor",myrank," opened file ITHEP"
5156 call getenv_loc('ROTPAR',rotname)
5157 open (irotam,file=rotname,status='old',action='read')
5158 ! print *,"Processor",myrank," opened file IROTAM"
5159 call getenv_loc('TORPAR',torname)
5160 open (itorp,file=torname,status='old',action='read')
5161 ! print *,"Processor",myrank," opened file ITORP"
5162 call getenv_loc('TORDPAR',tordname)
5163 open (itordp,file=tordname,status='old',action='read')
5164 ! print *,"Processor",myrank," opened file ITORDP"
5165 call getenv_loc('SCCORPAR',sccorname)
5166 open (isccor,file=sccorname,status='old',action='read')
5167 ! print *,"Processor",myrank," opened file ISCCOR"
5168 call getenv_loc('FOURIER',fouriername)
5169 open (ifourier,file=fouriername,status='old',action='read')
5170 ! print *,"Processor",myrank," opened file IFOURIER"
5171 call getenv_loc('ELEPAR',elename)
5172 open (ielep,file=elename,status='old',action='read')
5173 ! print *,"Processor",myrank," opened file IELEP"
5174 call getenv_loc('SIDEPAR',sidename)
5175 open (isidep,file=sidename,status='old',action='read')
5177 call getenv_loc('THETPAR_NUCL',thetname_nucl)
5178 open (ithep_nucl,file=thetname_nucl,status='old',action='read')
5179 call getenv_loc('ROTPAR_NUCL',rotname_nucl)
5180 open (irotam_nucl,file=rotname_nucl,status='old',action='read')
5181 call getenv_loc('TORPAR_NUCL',torname_nucl)
5182 open (itorp_nucl,file=torname_nucl,status='old',action='read')
5183 call getenv_loc('TORDPAR_NUCL',tordname_nucl)
5184 open (itordp_nucl,file=tordname_nucl,status='old',action='read')
5185 call getenv_loc('SIDEPAR_NUCL',sidename_nucl)
5186 open (isidep_nucl,file=sidename_nucl,status='old',action='read')
5188 call getenv_loc('LIPTRANPAR',liptranname)
5189 open (iliptranpar,file=liptranname,status='old',action='read')
5190 call getenv_loc('TUBEPAR',tubename)
5191 open (itube,file=tubename,status='old',action='read')
5192 call getenv_loc('IONPAR',ionname)
5193 open (iion,file=ionname,status='old',action='read')
5195 ! print *,"Processor",myrank," opened file ISIDEP"
5196 ! print *,"Processor",myrank," opened parameter files"
5198 open(1,file=pref_orig(:ilen(pref_orig))//'.inp',status='old')
5199 open (9,file=prefix(:ilen(prefix))//'.intin',status='unknown')
5200 ! open (18,file=prefix(:ilen(prefix))//'.entin',status='unknown')
5201 ! Get parameter filenames and open the parameter files.
5202 call getenv_loc('BONDPAR',bondname)
5203 open (ibond,file=bondname,status='old')
5204 call getenv_loc('BONDPAR_NUCL',bondname_nucl)
5205 open (ibond_nucl,file=bondname_nucl,status='old')
5207 call getenv_loc('THETPAR',thetname)
5208 open (ithep,file=thetname,status='old')
5209 call getenv_loc('ROTPAR',rotname)
5210 open (irotam,file=rotname,status='old')
5211 call getenv_loc('TORPAR',torname)
5212 open (itorp,file=torname,status='old')
5213 call getenv_loc('TORDPAR',tordname)
5214 open (itordp,file=tordname,status='old')
5215 call getenv_loc('SCCORPAR',sccorname)
5216 open (isccor,file=sccorname,status='old')
5217 call getenv_loc('FOURIER',fouriername)
5218 open (ifourier,file=fouriername,status='old')
5219 call getenv_loc('ELEPAR',elename)
5220 open (ielep,file=elename,status='old')
5221 call getenv_loc('SIDEPAR',sidename)
5222 open (isidep,file=sidename,status='old')
5224 open (ithep_nucl,file=thetname_nucl,status='old')
5225 call getenv_loc('ROTPAR_NUCL',rotname_nucl)
5226 open (irotam_nucl,file=rotname_nucl,status='old')
5227 call getenv_loc('TORPAR_NUCL',torname_nucl)
5228 open (itorp_nucl,file=torname_nucl,status='old')
5229 call getenv_loc('TORDPAR_NUCL',tordname_nucl)
5230 open (itordp_nucl,file=tordname_nucl,status='old')
5231 call getenv_loc('SIDEPAR_NUCL',sidename_nucl)
5232 open (isidep_nucl,file=sidename_nucl,status='old')
5234 call getenv_loc('LIPTRANPAR',liptranname)
5235 open (iliptranpar,file=liptranname,status='old')
5236 call getenv_loc('TUBEPAR',tubename)
5237 open (itube,file=tubename,status='old')
5238 call getenv_loc('IONPAR',ionname)
5239 open (iion,file=ionname,status='old')
5241 open(1,file=pref_orig(:ilen(pref_orig))//'.inp',status='old',&
5243 open (9,file=prefix(:ilen(prefix))//'.intin',status='unknown')
5244 ! open (18,file=prefix(:ilen(prefix))//'.entin',status='unknown')
5245 ! Get parameter filenames and open the parameter files.
5246 call getenv_loc('BONDPAR',bondname)
5247 open (ibond,file=bondname,status='old',action='read')
5248 call getenv_loc('BONDPAR_NUCL',bondname_nucl)
5249 open (ibond_nucl,file=bondname_nucl,status='old',action='read')
5250 call getenv_loc('THETPAR',thetname)
5251 open (ithep,file=thetname,status='old',action='read')
5252 call getenv_loc('ROTPAR',rotname)
5253 open (irotam,file=rotname,status='old',action='read')
5254 call getenv_loc('TORPAR',torname)
5255 open (itorp,file=torname,status='old',action='read')
5256 call getenv_loc('TORDPAR',tordname)
5257 open (itordp,file=tordname,status='old',action='read')
5258 call getenv_loc('SCCORPAR',sccorname)
5259 open (isccor,file=sccorname,status='old',action='read')
5261 call getenv_loc('THETPARPDB',thetname_pdb)
5262 print *,"thetname_pdb ",thetname_pdb
5263 open (ithep_pdb,file=thetname_pdb,status='old',action='read')
5264 print *,ithep_pdb," opened"
5266 call getenv_loc('FOURIER',fouriername)
5267 open (ifourier,file=fouriername,status='old',readonly)
5268 call getenv_loc('ELEPAR',elename)
5269 open (ielep,file=elename,status='old',readonly)
5270 call getenv_loc('SIDEPAR',sidename)
5271 open (isidep,file=sidename,status='old',readonly)
5273 call getenv_loc('THETPAR_NUCL',thetname_nucl)
5274 open (ithep_nucl,file=thetname_nucl,status='old',action='read')
5275 call getenv_loc('ROTPAR_NUCL',rotname_nucl)
5276 open (irotam_nucl,file=rotname_nucl,status='old',action='read')
5277 call getenv_loc('TORPAR_NUCL',torname_nucl)
5278 open (itorp_nucl,file=torname_nucl,status='old',action='read')
5279 call getenv_loc('TORDPAR_NUCL',tordname_nucl)
5280 open (itordp_nucl,file=tordname_nucl,status='old',action='read')
5281 call getenv_loc('SIDEPAR_NUCL',sidename_nucl)
5282 open (isidep_nucl,file=sidename_nucl,status='old',action='read')
5283 call getenv_loc('SIDEPAR_SCBASE',sidename_scbase)
5284 open (isidep_scbase,file=sidename_scbase,status='old',action='read')
5285 call getenv_loc('PEPPAR_PEPBASE',pepname_pepbase)
5286 open (isidep_pepbase,file=pepname_pepbase,status='old',action='read')
5287 call getenv_loc('SCPAR_PHOSPH',pepname_scpho)
5288 open (isidep_scpho,file=pepname_scpho,status='old',action='read')
5289 call getenv_loc('PEPPAR_PHOSPH',pepname_peppho)
5290 open (isidep_peppho,file=pepname_peppho,status='old',action='read')
5293 call getenv_loc('LIPTRANPAR',liptranname)
5294 open (iliptranpar,file=liptranname,status='old',action='read')
5295 call getenv_loc('TUBEPAR',tubename)
5296 open (itube,file=tubename,status='old',action='read')
5297 call getenv_loc('IONPAR',ionname)
5298 open (iion,file=ionname,status='old',action='read')
5301 call getenv_loc('ROTPARPDB',rotname_pdb)
5302 open (irotam_pdb,file=rotname_pdb,status='old',action='read')
5305 call getenv_loc('SCPPAR_NUCL',scpname_nucl)
5306 #if defined(WINIFL) || defined(WINPGI)
5307 open (iscpp_nucl,file=scpname_nucl,status='old',readonly,shared)
5308 #elif (defined CRAY) || (defined AIX)
5309 open (iscpp_nucl,file=scpname_nucl,status='old',action='read')
5311 open (iscpp_nucl,file=scpname_nucl,status='old')
5313 open (iscpp_nucl,file=scpname_nucl,status='old',action='read')
5318 ! 8/9/01 In the newest version SCp interaction constants are read from a file
5319 ! Use -DOLDSCP to use hard-coded constants instead.
5321 call getenv_loc('SCPPAR',scpname)
5322 #if defined(WINIFL) || defined(WINPGI)
5323 open (iscpp,file=scpname,status='old',readonly,shared)
5324 #elif (defined CRAY) || (defined AIX)
5325 open (iscpp,file=scpname,status='old',action='read')
5327 open (iscpp,file=scpname,status='old')
5329 open (iscpp,file=scpname,status='old',action='read')
5332 call getenv_loc('PATTERN',patname)
5333 #if defined(WINIFL) || defined(WINPGI)
5334 open (icbase,file=patname,status='old',readonly,shared)
5335 #elif (defined CRAY) || (defined AIX)
5336 open (icbase,file=patname,status='old',action='read')
5338 open (icbase,file=patname,status='old')
5340 open (icbase,file=patname,status='old',action='read')
5343 ! Open output file only for CG processes
5344 ! print *,"Processor",myrank," fg_rank",fg_rank
5345 if (fg_rank.eq.0) then
5347 if (nodes.eq.1) then
5350 npos = dlog10(dfloat(nodes-1))+1
5352 if (npos.lt.3) npos=3
5353 write (liczba,'(i1)') npos
5354 form = '(bz,i'//liczba(:ilen(liczba))//'.'//liczba(:ilen(liczba)) &
5356 write (liczba,form) me
5357 outname=prefix(:lenpre)//'.out_'//pot(:lenpot)// &
5358 liczba(:ilen(liczba))
5359 intname=prefix(:lenpre)//'_'//pot(:lenpot)//liczba(:ilen(liczba)) &
5361 pdbname=prefix(:lenpre)//'_'//pot(:lenpot)//liczba(:ilen(liczba)) &
5363 mol2name=prefix(:lenpre)//'_'//pot(:lenpot)// &
5364 liczba(:ilen(liczba))//'.mol2'
5365 statname=prefix(:lenpre)//'_'//pot(:lenpot)// &
5366 liczba(:ilen(liczba))//'.stat'
5368 call copy_to_tmp(pref_orig(:ilen(pref_orig))//'_'//pot(:lenpot) &
5369 //liczba(:ilen(liczba))//'.stat')
5370 rest2name=prefix(:ilen(prefix))//"_"//liczba(:ilen(liczba)) &
5373 qname=prefix(:lenpre)//'_'//pot(:lenpot)// &
5374 liczba(:ilen(liczba))//'.const'
5379 outname=prefix(:lenpre)//'.out_'//pot(:lenpot)
5380 intname=prefix(:lenpre)//'_'//pot(:lenpot)//'.int'
5381 pdbname=prefix(:lenpre)//'_'//pot(:lenpot)//'.pdb'
5382 mol2name=prefix(:lenpre)//'_'//pot(:lenpot)//'.mol2'
5383 statname=prefix(:lenpre)//'_'//pot(:lenpot)//'.stat'
5385 call copy_to_tmp(pref_orig(:ilen(pref_orig))//'_'//pot(:lenpot)// &
5387 rest2name=prefix(:ilen(prefix))//'.rst'
5389 qname=prefix(:lenpre)//'_'//pot(:lenpot)//'.const'
5392 #if defined(AIX) || defined(PGI)
5393 if (me.eq.king .or. .not. out1file) &
5394 open(iout,file=outname,status='unknown')
5396 if (fg_rank.gt.0) then
5397 write (liczba,'(i3.3)') myrank/nfgtasks
5398 write (ll,'(bz,i3.3)') fg_rank
5399 open(iout,file="debug"//liczba(:ilen(liczba))//"."//ll,&
5404 open(igeom,file=intname,status='unknown',position='append')
5405 open(ipdb,file=pdbname,status='unknown')
5406 open(imol2,file=mol2name,status='unknown')
5407 open(istat,file=statname,status='unknown',position='append')
5409 !1out open(iout,file=outname,status='unknown')
5412 if (me.eq.king .or. .not.out1file) &
5413 open(iout,file=outname,status='unknown')
5415 if (fg_rank.gt.0) then
5416 write (liczba,'(i3.3)') myrank/nfgtasks
5417 write (ll,'(bz,i3.3)') fg_rank
5418 open(iout,file="debug"//liczba(:ilen(liczba))//"."//ll,&
5423 open(igeom,file=intname,status='unknown',access='append')
5424 open(ipdb,file=pdbname,status='unknown')
5425 open(imol2,file=mol2name,status='unknown')
5426 open(istat,file=statname,status='unknown',access='append')
5428 !1out open(iout,file=outname,status='unknown')
5431 csa_rbank=prefix(:lenpre)//'.CSA.rbank'
5432 csa_seed=prefix(:lenpre)//'.CSA.seed'
5433 csa_history=prefix(:lenpre)//'.CSA.history'
5434 csa_bank=prefix(:lenpre)//'.CSA.bank'
5435 csa_bank1=prefix(:lenpre)//'.CSA.bank1'
5436 csa_alpha=prefix(:lenpre)//'.CSA.alpha'
5437 csa_alpha1=prefix(:lenpre)//'.CSA.alpha1'
5438 !!bankt csa_bankt=prefix(:lenpre)//'.CSA.bankt'
5439 csa_int=prefix(:lenpre)//'.int'
5440 csa_bank_reminimized=prefix(:lenpre)//'.CSA.bank_reminimized'
5441 csa_native_int=prefix(:lenpre)//'.CSA.native.int'
5442 csa_in=prefix(:lenpre)//'.CSA.in'
5443 ! print *,"Processor",myrank,"fg_rank",fg_rank," opened files"
5446 write (iout,'(80(1h-))')
5447 write (iout,'(30x,a)') "FILE ASSIGNMENT"
5448 write (iout,'(80(1h-))')
5449 write (iout,*) "Input file : ",&
5450 pref_orig(:ilen(pref_orig))//'.inp'
5451 write (iout,*) "Output file : ",&
5452 outname(:ilen(outname))
5454 write (iout,*) "Sidechain potential file : ",&
5455 sidename(:ilen(sidename))
5457 write (iout,*) "SCp potential file : ",&
5458 scpname(:ilen(scpname))
5460 write (iout,*) "Electrostatic potential file : ",&
5461 elename(:ilen(elename))
5462 write (iout,*) "Cumulant coefficient file : ",&
5463 fouriername(:ilen(fouriername))
5464 write (iout,*) "Torsional parameter file : ",&
5465 torname(:ilen(torname))
5466 write (iout,*) "Double torsional parameter file : ",&
5467 tordname(:ilen(tordname))
5468 write (iout,*) "SCCOR parameter file : ",&
5469 sccorname(:ilen(sccorname))
5470 write (iout,*) "Bond & inertia constant file : ",&
5471 bondname(:ilen(bondname))
5472 write (iout,*) "Bending parameter file : ",&
5473 thetname(:ilen(thetname))
5474 write (iout,*) "Rotamer parameter file : ",&
5475 rotname(:ilen(rotname))
5478 write (iout,*) "Thetpdb parameter file : ",&
5479 thetname_pdb(:ilen(thetname_pdb))
5482 write (iout,*) "Threading database : ",&
5483 patname(:ilen(patname))
5485 write (iout,*)" DIRTMP : ",&
5487 write (iout,'(80(1h-))')
5490 end subroutine openunits
5491 !-----------------------------------------------------------------------------
5494 use geometry_data, only: nres,dc
5496 ! implicit real*8 (a-h,o-z)
5497 ! include 'DIMENSIONS'
5498 ! include 'COMMON.CHAIN'
5499 ! include 'COMMON.IOUNITS'
5500 ! include 'COMMON.MD'
5503 ! real(kind=8) :: var,ene
5505 open(irest2,file=rest2name,status='unknown')
5506 read(irest2,*) totT,EK,potE,totE,t_bath
5509 ! AL 4/17/17: Now reading d_t(0,:) too
5511 read(irest2,'(3e15.5)') (d_t(j,i),j=1,3)
5514 ! AL 4/17/17: Now reading d_c(0,:) too
5516 read(irest2,'(3e15.5)') (dc(j,i),j=1,3)
5519 read (irest2,*) iset
5523 end subroutine readrst
5524 !-----------------------------------------------------------------------------
5525 subroutine read_fragments
5529 use control_data, only:out1file
5532 ! implicit real*8 (a-h,o-z)
5533 ! include 'DIMENSIONS'
5537 ! include 'COMMON.SETUP'
5538 ! include 'COMMON.CHAIN'
5539 ! include 'COMMON.IOUNITS'
5540 ! include 'COMMON.MD'
5541 ! include 'COMMON.CONTROL'
5544 ! real(kind=8) :: var,ene
5546 read(inp,*) nset,nfrag,npair,nfrag_back
5548 !el from module energy
5549 ! if(.not.allocated(mset)) allocate(mset(nset)) !(maxprocs/20)
5550 if(.not.allocated(wfrag_back)) then
5551 allocate(wfrag_back(3,nfrag_back,nset)) !(3,maxfrag_back,maxprocs/20)
5552 allocate(ifrag_back(3,nfrag_back,nset)) !(3,maxfrag_back,maxprocs/20)
5554 allocate(qinfrag(nfrag,nset),wfrag(nfrag,nset)) !(50,maxprocs/20)
5555 allocate(ifrag(2,nfrag,nset)) !(2,50,maxprocs/20)
5557 allocate(qinpair(npair,nset),wpair(npair,nset)) !(100,maxprocs/20)
5558 allocate(ipair(2,npair,nset)) !(2,100,maxprocs/20)
5561 if(me.eq.king.or..not.out1file) &
5562 write(iout,*) "nset",nset," nfrag",nfrag," npair",npair,&
5563 " nfrag_back",nfrag_back
5565 read(inp,*) mset(iset)
5567 read(inp,*) wfrag(i,iset),ifrag(1,i,iset),ifrag(2,i,iset),&
5569 if(me.eq.king.or..not.out1file) &
5570 write(iout,*) "R ",i,wfrag(i,iset),ifrag(1,i,iset),&
5571 ifrag(2,i,iset), qinfrag(i,iset)
5574 read(inp,*) wpair(i,iset),ipair(1,i,iset),ipair(2,i,iset),&
5576 if(me.eq.king.or..not.out1file) &
5577 write(iout,*) "R ",i,wpair(i,iset),ipair(1,i,iset),&
5578 ipair(2,i,iset), qinpair(i,iset)
5581 read(inp,*) wfrag_back(1,i,iset),wfrag_back(2,i,iset),&
5582 wfrag_back(3,i,iset),&
5583 ifrag_back(1,i,iset),ifrag_back(2,i,iset)
5584 if(me.eq.king.or..not.out1file) &
5585 write(iout,*) "A",i,wfrag_back(1,i,iset),wfrag_back(2,i,iset),&
5586 wfrag_back(3,i,iset),ifrag_back(1,i,iset),ifrag_back(2,i,iset)
5590 end subroutine read_fragments
5591 !-----------------------------------------------------------------------------
5593 !-----------------------------------------------------------------------------
5597 ! implicit real*8 (a-h,o-z)
5598 ! include 'DIMENSIONS'
5599 ! include 'COMMON.CSA'
5600 ! include 'COMMON.BANK'
5601 ! include 'COMMON.IOUNITS'
5603 ! integer :: ntf,ik,iw_pdb
5604 ! real(kind=8) :: var,ene
5606 open(icsa_in,file=csa_in,status="old",err=100)
5607 read(icsa_in,*) nconf
5608 read(icsa_in,*) jstart,jend
5609 read(icsa_in,*) nstmax
5610 read(icsa_in,*) n1,n2,n3,n4,n5,n6,n7,n8,is1,is2
5611 read(icsa_in,*) nran0,nran1,irr
5612 read(icsa_in,*) nseed
5613 read(icsa_in,*) ntotal,cut1,cut2
5614 read(icsa_in,*) estop
5615 read(icsa_in,*) icmax,irestart
5616 read(icsa_in,*) ntbankm,dele,difcut
5617 read(icsa_in,*) iref,rmscut,pnccut
5618 read(icsa_in,*) ndiff
5625 end subroutine csa_read
5626 !-----------------------------------------------------------------------------
5627 subroutine initial_write
5630 ! implicit real*8 (a-h,o-z)
5631 ! include 'DIMENSIONS'
5632 ! include 'COMMON.CSA'
5633 ! include 'COMMON.BANK'
5634 ! include 'COMMON.IOUNITS'
5636 ! integer :: ntf,ik,iw_pdb
5637 ! real(kind=8) :: var,ene
5639 open(icsa_seed,file=csa_seed,status="unknown")
5640 write(icsa_seed,*) "seed"
5642 #if defined(AIX) || defined(PGI)
5643 open(icsa_history,file=csa_history,status="unknown",&
5646 open(icsa_history,file=csa_history,status="unknown",&
5649 write(icsa_history,*) nconf
5650 write(icsa_history,*) jstart,jend
5651 write(icsa_history,*) nstmax
5652 write(icsa_history,*) n1,n2,n3,n4,n5,n6,n7,n8,is1,is2
5653 write(icsa_history,*) nran0,nran1,irr
5654 write(icsa_history,*) nseed
5655 write(icsa_history,*) ntotal,cut1,cut2
5656 write(icsa_history,*) estop
5657 write(icsa_history,*) icmax,irestart
5658 write(icsa_history,*) ntbankm,dele,difcut
5659 write(icsa_history,*) iref,rmscut,pnccut
5660 write(icsa_history,*) ndiff
5662 write(icsa_history,*)
5665 open(icsa_bank1,file=csa_bank1,status="unknown")
5666 write(icsa_bank1,*) 0
5670 end subroutine initial_write
5671 !-----------------------------------------------------------------------------
5672 subroutine restart_write
5675 ! implicit real*8 (a-h,o-z)
5676 ! include 'DIMENSIONS'
5677 ! include 'COMMON.IOUNITS'
5678 ! include 'COMMON.CSA'
5679 ! include 'COMMON.BANK'
5681 ! integer :: ntf,ik,iw_pdb
5682 ! real(kind=8) :: var,ene
5684 #if defined(AIX) || defined(PGI)
5685 open(icsa_history,file=csa_history,position="append")
5687 open(icsa_history,file=csa_history,access="append")
5689 write(icsa_history,*)
5690 write(icsa_history,*) "This is restart"
5691 write(icsa_history,*)
5692 write(icsa_history,*) nconf
5693 write(icsa_history,*) jstart,jend
5694 write(icsa_history,*) nstmax
5695 write(icsa_history,*) n1,n2,n3,n4,n5,n6,n7,n8,is1,is2
5696 write(icsa_history,*) nran0,nran1,irr
5697 write(icsa_history,*) nseed
5698 write(icsa_history,*) ntotal,cut1,cut2
5699 write(icsa_history,*) estop
5700 write(icsa_history,*) icmax,irestart
5701 write(icsa_history,*) ntbankm,dele,difcut
5702 write(icsa_history,*) iref,rmscut,pnccut
5703 write(icsa_history,*) ndiff
5704 write(icsa_history,*)
5705 write(icsa_history,*) "irestart is: ", irestart
5707 write(icsa_history,*)
5711 end subroutine restart_write
5712 !-----------------------------------------------------------------------------
5714 !-----------------------------------------------------------------------------
5715 subroutine write_pdb(npdb,titelloc,ee)
5717 ! implicit real*8 (a-h,o-z)
5718 ! include 'DIMENSIONS'
5719 ! include 'COMMON.IOUNITS'
5720 character(len=50) :: titelloc1
5721 character*(*) :: titelloc
5722 character(len=3) :: zahl
5723 character(len=5) :: liczba5
5725 integer :: npdb !,ilen
5729 ! real(kind=8) :: var,ene
5733 if (npdb.lt.1000) then
5734 call numstr(npdb,zahl)
5735 open(ipdb,file=prefix(:lenpre)//'@@'//zahl//'.pdb')
5737 if (npdb.lt.10000) then
5738 write(liczba5,'(i1,i4)') 0,npdb
5740 write(liczba5,'(i5)') npdb
5742 open(ipdb,file=prefix(:lenpre)//'@@'//liczba5//'.pdb')
5744 call pdbout(ee,titelloc1,ipdb)
5747 end subroutine write_pdb
5748 !-----------------------------------------------------------------------------
5750 !-----------------------------------------------------------------------------
5751 subroutine write_thread_summary
5752 ! Thread the sequence through a database of known structures
5753 use control_data, only: refstr
5755 use energy_data, only: n_ene_comp
5757 ! implicit real*8 (a-h,o-z)
5758 ! include 'DIMENSIONS'
5760 use MPI_data !include 'COMMON.INFO'
5763 ! include 'COMMON.CONTROL'
5764 ! include 'COMMON.CHAIN'
5765 ! include 'COMMON.DBASE'
5766 ! include 'COMMON.INTERACT'
5767 ! include 'COMMON.VAR'
5768 ! include 'COMMON.THREAD'
5769 ! include 'COMMON.FFIELD'
5770 ! include 'COMMON.SBRIDGE'
5771 ! include 'COMMON.HEADER'
5772 ! include 'COMMON.NAMES'
5773 ! include 'COMMON.IOUNITS'
5774 ! include 'COMMON.TIME1'
5776 integer,dimension(maxthread) :: ip
5777 real(kind=8),dimension(0:n_ene) :: energia
5779 integer :: i,j,ii,jj,ipj,ik,kk,ist
5780 real(kind=8) :: enet,etot,rmsnat,rms,frac,frac_nn
5782 write (iout,'(30x,a/)') &
5783 ' *********** Summary threading statistics ************'
5784 write (iout,'(a)') 'Initial energies:'
5785 write (iout,'(a4,2x,a12,14a14,3a8)') &
5786 'No','seq',(ename(print_order(i)),i=1,nprint_ene),'ETOT',&
5787 'RMSnat','NatCONT','NNCONT','RMS'
5788 ! Energy sort patterns
5793 enet=ener(n_ene-1,ip(i))
5796 if (ener(n_ene-1,ip(j)).lt.enet) then
5798 enet=ener(n_ene-1,ip(j))
5810 ist=nres_base(2,ii)+ipatt(2,i)
5812 energia(i)=ener0(kk,i)
5814 etot=ener0(n_ene_comp+1,i)
5815 rmsnat=ener0(n_ene_comp+2,i)
5816 rms=ener0(n_ene_comp+3,i)
5817 frac=ener0(n_ene_comp+4,i)
5818 frac_nn=ener0(n_ene_comp+5,i)
5821 write (iout,'(i4,2x,a8,i4,14(1pe14.5),0pf8.3,f8.5,f8.5,f8.3)') &
5822 i,str_nam(ii),ist+1,&
5823 (energia(print_order(kk)),kk=1,nprint_ene),&
5824 etot,rmsnat,frac,frac_nn,rms
5826 write (iout,'(i4,2x,a8,i4,14(1pe14.5),0pf8.3)') &
5827 i,str_nam(ii),ist+1,&
5828 (energia(print_order(kk)),kk=1,nprint_ene),etot
5831 write (iout,'(//a)') 'Final energies:'
5832 write (iout,'(a4,2x,a12,17a14,3a8)') &
5833 'No','seq',(ename(print_order(kk)),kk=1,nprint_ene),'ETOT',&
5834 'RMSnat','NatCONT','NNCONT','RMS'
5838 ist=nres_base(2,ii)+ipatt(2,i)
5840 energia(kk)=ener(kk,ik)
5842 etot=ener(n_ene_comp+1,i)
5843 rmsnat=ener(n_ene_comp+2,i)
5844 rms=ener(n_ene_comp+3,i)
5845 frac=ener(n_ene_comp+4,i)
5846 frac_nn=ener(n_ene_comp+5,i)
5847 write (iout,'(i4,2x,a8,i4,14(1pe14.5),0pf8.3,f8.5,f8.5,f8.3)') &
5848 i,str_nam(ii),ist+1,&
5849 (energia(print_order(kk)),kk=1,nprint_ene),&
5850 etot,rmsnat,frac,frac_nn,rms
5852 write (iout,'(/a/)') 'IEXAM array:'
5853 write (iout,'(i5)') nexcl
5855 write (iout,'(2i5)') iexam(1,i),iexam(2,i)
5857 write (iout,'(/a,1pe14.4/a,1pe14.4/)') &
5858 'Max. time for threading step ',max_time_for_thread,&
5859 'Average time for threading step: ',ave_time_for_thread
5861 end subroutine write_thread_summary
5862 !-----------------------------------------------------------------------------
5863 subroutine write_stat_thread(ithread,ipattern,ist)
5865 use energy_data, only: n_ene_comp
5867 ! implicit real*8 (a-h,o-z)
5868 ! include "DIMENSIONS"
5869 ! include "COMMON.CONTROL"
5870 ! include "COMMON.IOUNITS"
5871 ! include "COMMON.THREAD"
5872 ! include "COMMON.FFIELD"
5873 ! include "COMMON.DBASE"
5874 ! include "COMMON.NAMES"
5875 real(kind=8),dimension(0:n_ene) :: energia
5877 integer :: ithread,ipattern,ist,i
5878 real(kind=8) :: etot,rmsnat,rms,frac,frac_nn
5880 #if defined(AIX) || defined(PGI)
5881 open(istat,file=statname,position='append')
5883 open(istat,file=statname,access='append')
5886 energia(i)=ener(i,ithread)
5888 etot=ener(n_ene_comp+1,ithread)
5889 rmsnat=ener(n_ene_comp+2,ithread)
5890 rms=ener(n_ene_comp+3,ithread)
5891 frac=ener(n_ene_comp+4,ithread)
5892 frac_nn=ener(n_ene_comp+5,ithread)
5893 write (istat,'(i4,2x,a8,i4,14(1pe14.5),0pf8.3,f8.5,f8.5,f8.3)') &
5894 ithread,str_nam(ipattern),ist+1,&
5895 (energia(print_order(i)),i=1,nprint_ene),&
5896 etot,rmsnat,frac,frac_nn,rms
5899 end subroutine write_stat_thread
5900 !-----------------------------------------------------------------------------
5902 !-----------------------------------------------------------------------------
5903 end module io_config