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))
3254 if (.not.allocated(sigmacat)) allocate(sigmacat(0:ntyp1,0:ntyp1))
3255 if (.not.allocated(chicat)) allocate(chicat(ntyp1,ntyp1)) !(ntyp,ntyp)
3257 ! i to SC, j to jon, isideocat - nazwa pliku z ktorego czytam parametry
3258 if (oldion.eq.0) then
3259 do i=1,ntyp_molec(5)
3260 read(iion,*) msc(i,5),restok(i,5)
3261 print *,msc(i,5),restok(i,5)
3266 do j=1,ntyp_molec(5)
3267 ! write (*,*) "Im in ALAB", i, " ", j
3269 epscat(i,j),sigmacat(i,j),chicat(i,j),chicat(j,i),chippcat(i,j),chippcat(j,i), &
3270 (alphasurcat(k,i,j),k=1,4),sigmap1cat(i,j),sigmap2cat(i,j),&
3271 chiscat(i,j),chiscat(j,i), &
3272 dheadcat(1,1,i,j),dheadcat(1,2,i,j),dheadcat(2,1,i,j),dheadcat(2,2,i,j),&
3273 dtailcat(1,i,j),dtailcat(2,i,j), &
3274 epsheadcat(i,j),sig0headcat(i,j), &
3276 rborncat(i,j),rborncat(j,i),(wqdipcat(k,i,j),k=1,2), &
3277 alphapolcat(i,j),alphapolcat(j,i), &
3278 (alphisocat(k,i,j),k=1,4),sigiso1cat(i,j),sigiso2cat(i,j),epsintabcat(i,j),debaykapcat(i,j)
3279 ! print *,eps(i,j),sigma(i,j),"SIGMAP",i,j,sigmap1(i,j),sigmap2(j,i)
3286 write (iout,'(/a)') "Disulfide bridge parameters:"
3287 write (iout,'(a,f10.2)') 'S-S bridge energy: ',ebr
3288 write (iout,'(2(a,f10.2))') 'd0cm:',d0cm,' akcm:',akcm
3289 write (iout,'(2(a,f10.2))') 'akth:',akth,' akct:',akct
3290 write (iout,'(3(a,f10.2))') 'v1ss:',v1ss,' v2ss:',v2ss,&
3293 if (shield_mode.gt.0) then
3294 pi=4.0D0*datan(1.0D0)
3295 !C VSolvSphere the volume of solving sphere
3297 !C rpp(1,1) is the energy r0 for peptide group contact and will be used for it
3298 !C there will be no distinction between proline peptide group and normal peptide
3299 !C group in case of shielding parameters
3300 VSolvSphere=4.0/3.0*pi*(4.50d0)**3
3301 VSolvSphere_div=VSolvSphere-4.0/3.0*pi*(4.50/2.0)**3
3302 write (iout,*) VSolvSphere,VSolvSphere_div
3303 !C long axis of side chain
3305 long_r_sidechain(i)=vbldsc0(1,i)
3306 ! if (scelemode.eq.0) then
3307 short_r_sidechain(i)=sigma(i,i)/sqrt(2.0)
3308 if (short_r_sidechain(i).eq.0.0) short_r_sidechain(i)=0.2
3310 ! short_r_sidechain(i)=sigma(i,i)
3312 write(iout,*) "parame for long and short axis",i,vbldsc0(1,i),&
3319 111 write (iout,*) "Error reading bending energy parameters."
3321 112 write (iout,*) "Error reading rotamer energy parameters."
3323 113 write (iout,*) "Error reading torsional energy parameters."
3325 114 write (iout,*) "Error reading double torsional energy parameters."
3327 115 write (iout,*) &
3328 "Error reading cumulant (multibody energy) parameters."
3330 116 write (iout,*) "Error reading electrostatic energy parameters."
3332 117 write (iout,*) "Error reading side chain interaction parameters."
3334 118 write (iout,*) "Error reading SCp interaction parameters."
3336 119 write (iout,*) "Error reading SCCOR parameters"
3338 121 write (iout,*) "Error in Czybyshev parameters"
3341 call MPI_Finalize(Ierror)
3345 end subroutine parmread
3347 !-----------------------------------------------------------------------------
3349 !-----------------------------------------------------------------------------
3350 subroutine printmat(ldim,m,n,iout,key,a)
3353 character(len=3),dimension(n) :: key
3354 real(kind=8),dimension(ldim,n) :: a
3356 integer :: i,j,k,m,iout,nlim
3360 write (iout,1000) (key(k),k=i,nlim)
3362 1000 format (/5x,8(6x,a3))
3363 1020 format (/80(1h-)/)
3365 write (iout,1010) key(j),(a(j,k),k=i,nlim)
3368 1010 format (a3,2x,8(f9.4))
3370 end subroutine printmat
3371 !-----------------------------------------------------------------------------
3373 !-----------------------------------------------------------------------------
3375 ! Read the PDB file and convert the peptide geometry into virtual-chain
3378 use energy_data, only: itype,istype
3382 ! use control, only: rescode,sugarcode
3383 ! implicit real*8 (a-h,o-z)
3384 ! include 'DIMENSIONS'
3385 ! include 'COMMON.LOCAL'
3386 ! include 'COMMON.VAR'
3387 ! include 'COMMON.CHAIN'
3388 ! include 'COMMON.INTERACT'
3389 ! include 'COMMON.IOUNITS'
3390 ! include 'COMMON.GEO'
3391 ! include 'COMMON.NAMES'
3392 ! include 'COMMON.CONTROL'
3393 ! include 'COMMON.DISTFIT'
3394 ! include 'COMMON.SETUP'
3395 integer :: i,j,ibeg,ishift1,ires,iii,ires_old,ishift,k!,ity!,&
3397 logical :: lprn=.true.,fail
3398 real(kind=8),dimension(3) :: e1,e2,e3
3399 real(kind=8) :: dcj,efree_temp
3400 character(len=3) :: seq,res,res2
3401 character(len=5) :: atom
3402 character(len=80) :: card
3403 real(kind=8),dimension(3,20) :: sccor
3404 integer :: kkk,lll,icha,kupa,molecule,counter,seqalingbegin !rescode,
3405 integer :: isugar,molecprev,firstion
3406 character*1 :: sugar
3408 real(kind=8),dimension(3) :: ccc
3410 integer,dimension(2,maxres/3) :: hfrag_alloc
3411 integer,dimension(4,maxres/3) :: bfrag_alloc
3412 real(kind=8),dimension(3,maxres2+2,maxperm) :: cref_alloc !(3,maxres2+2,maxperm)
3413 real(kind=8),dimension(:,:), allocatable :: c_temporary
3414 integer,dimension(:,:) , allocatable :: itype_temporary
3415 integer,dimension(:),allocatable :: istype_temp
3422 ! write (2,*) "UNRES_PDB",unres_pdb
3442 !-----------------------------
3443 allocate(hfrag(2,maxres/3)) !(2,maxres/3)
3444 allocate(bfrag(4,maxres/3)) !(4,maxres/3)
3445 if(.not. allocated(istype)) allocate(istype(maxres))
3447 read (ipdbin,'(a80)',end=10) card
3448 write (iout,'(a)') card
3449 if (card(:5).eq.'HELIX') then
3452 read(card(22:25),*) hfrag(1,nhfrag)
3453 read(card(34:37),*) hfrag(2,nhfrag)
3455 if (card(:5).eq.'SHEET') then
3458 read(card(24:26),*) bfrag(1,nbfrag)
3459 read(card(35:37),*) bfrag(2,nbfrag)
3460 !rc----------------------------------------
3461 !rc to be corrected !!!
3462 bfrag(3,nbfrag)=bfrag(1,nbfrag)
3463 bfrag(4,nbfrag)=bfrag(2,nbfrag)
3464 !rc----------------------------------------
3466 if (card(:3).eq.'END') then
3468 else if (card(:3).eq.'TER') then
3473 itype(ires_old,molecule)=ntyp1_molec(molecule)
3474 itype(ires_old-1,molecule)=ntyp1_molec(molecule)
3475 nres_molec(molecule)=nres_molec(molecule)+2
3477 ! write (iout,*) "Chain ended",ires,ishift,ires_old
3480 dc(j,ires)=sccor(j,iii)
3483 call sccenter(ires,iii,sccor)
3489 if (index(card,"FREE ENERGY").gt.0) read(card(35:),*) efree_temp
3490 ! Fish out the ATOM cards.
3491 ! write(iout,*) 'card',card(1:20)
3492 ! print *,"ATU ",card(1:6), CARD(3:6)
3494 if (index(card(1:4),'ATOM').gt.0) then
3495 read (card(12:16),*) atom
3496 ! write (iout,*) "! ",atom," !",ires
3497 ! if (atom.eq.'CA' .or. atom.eq.'CH3') then
3498 read (card(23:26),*) ires
3499 read (card(18:20),'(a3)') res
3500 ! write (iout,*) "ires",ires,ires-ishift+ishift1,
3501 ! & " ires_old",ires_old
3502 ! write (iout,*) "ishift",ishift," ishift1",ishift1
3503 ! write (iout,*) "IRES",ires-ishift+ishift1,ires_old
3504 if (ires-ishift+ishift1.ne.ires_old) then
3505 ! Calculate the CM of the preceding residue.
3506 ! if (ibeg.eq.0) call sccenter(ires,iii,sccor)
3508 ! write (iout,*) "Calculating sidechain center iii",iii
3511 dc(j,ires+ishift1-ishift-1)=sccor(j,iii)
3514 call sccenter(ires_old,iii,sccor)
3518 ! Start new residue.
3519 if (res.eq.'Cl-' .or. res.eq.'Na+') then
3522 else if (ibeg.eq.1) then
3523 write (iout,*) "BEG ires",ires
3525 if (res.ne.'GLY' .and. res.ne. 'ACE') then
3528 nres_molec(molecule)=nres_molec(molecule)+1
3530 ires=ires-ishift+ishift1
3532 ! write (iout,*) "ishift",ishift," ires",ires,&
3533 ! " ires_old",ires_old
3535 else if (ibeg.eq.2) then
3537 ishift=-ires_old+ires-1 !!!!!
3538 ishift1=ishift1-1 !!!!!
3539 ! write (iout,*) "New chain started",ires,ishift,ishift1,"!"
3540 ires=ires-ishift+ishift1
3541 ! print *,ires,ishift,ishift1
3545 ishift=ishift-(ires-ishift+ishift1-ires_old-1)
3546 ires=ires-ishift+ishift1
3549 ! print *,'atom',ires,atom
3550 if (res.eq.'ACE' .or. res.eq.'NHE') then
3553 if (atom.eq.'CA '.or.atom.eq.'N ') then
3555 itype(ires,molecule)=rescode(ires,res,0,molecule)
3557 ! nres_molec(molecule)=nres_molec(molecule)+1
3561 itype(ires,molecule)=rescode(ires,res2,0,molecule)
3562 ! nres_molec(molecule)=nres_molec(molecule)+1
3563 read (card(19:19),'(a1)') sugar
3564 isugar=sugarcode(sugar,ires)
3565 ! if (ibeg.eq.1) then
3569 ! print *,"ires=",ires,istype(ires)
3575 ires=ires-ishift+ishift1
3577 ! write (iout,*) "ires_old",ires_old," ires",ires
3578 if (card(27:27).eq."A" .or. card(27:27).eq."B") then
3581 ! write (2,*) "ires",ires," res ",res!," ity"!,ity
3582 if (atom.eq.'CA' .or. atom.eq.'CH3' .or. &
3583 res.eq.'NHE'.and.atom(:2).eq.'HN') then
3584 read(card(31:54),'(3f8.3)') (c(j,ires),j=1,3)
3585 ! print *,ires,ishift,ishift1
3586 ! write (iout,*) "backbone ",atom
3588 write (iout,'(2i3,2x,a,3f8.3)') &
3589 ires,itype(ires,1),res,(c(j,ires),j=1,3)
3592 nres_molec(molecule)=nres_molec(molecule)+1
3594 sccor(j,iii)=c(j,ires)
3596 else if (.not.unres_pdb .and. (atom.eq."C1'" .or. &
3597 atom.eq."C2'" .or. atom.eq."C3'" &
3598 .or. atom.eq."C4'" .or. atom.eq."O4'")) then
3599 read(card(31:54),'(3f8.3)') (ccc(j),j=1,3)
3600 !c write (2,'(i5,3f10.5)') ires,(ccc(j),j=1,3)
3601 ! print *,ires,ishift,ishift1
3605 ! sccor(j,iii)=c(j,ires)
3608 c(j,ires)=c(j,ires)+ccc(j)/5.0
3610 print *,counter,molecule
3611 if (counter.eq.5) then
3613 nres_molec(molecule)=nres_molec(molecule)+1
3616 ! sccor(j,iii)=c(j,ires)
3620 ! print *, "ATOM",atom(1:3)
3621 else if (atom.eq."C5'") then
3622 read (card(19:19),'(a1)') sugar
3623 isugar=sugarcode(sugar,ires)
3628 ! print *,ires,istype(ires)
3632 ! print *,"nres_molec(molecule)",nres_molec(molecule),ires
3633 read(card(31:54),'(3f8.3)') (c(j,ires),j=1,3)
3634 nres_molec(molecule)=nres_molec(molecule)+1
3635 print *,"nres_molec(molecule)",nres_molec(molecule),ires
3639 read(card(31:54),'(3f8.3)') (sccor(j,iii),j=1,3)
3641 else if ((atom.eq."C1'").and.unres_pdb) then
3643 read(card(31:54),'(3f8.3)') (sccor(j,iii),j=1,3)
3644 ! write (*,*) card(23:27),ires,itype(ires,1)
3645 else if (atom.ne.'O'.and.atom(1:1).ne.'H' .and. &
3646 atom.ne.'N' .and. atom.ne.'C' .and. &
3647 atom(:2).ne.'1H' .and. atom(:2).ne.'2H' .and. &
3648 atom.ne.'OXT' .and. atom(:2).ne.'3H' &
3649 .and. atom.ne.'P '.and. &
3650 atom(1:1).ne.'H' .and. &
3651 atom.ne.'OP1' .and. atom.ne.'OP2 '.and. atom.ne.'OP3'&
3653 ! write (iout,*) "sidechain ",atom
3654 ! write (iout,*) "sidechain ",atom,molecule,ires,atom(3:3)
3655 if ((molecule.ne.2).or.(atom(3:3).ne."'")) then
3656 ! write (iout,*) "sidechain ",atom,molecule,ires,atom(3:3)
3658 read(card(31:54),'(3f8.3)') (sccor(j,iii),j=1,3)
3661 ! print *,"IONS",ions,card(1:6)
3662 else if ((ions).and.(card(1:6).eq.'HETATM')) then
3663 if (firstion.eq.0) then
3667 dc(j,ires)=sccor(j,iii)
3670 call sccenter(ires,iii,sccor)
3673 read (card(12:16),*) atom
3674 ! print *,"HETATOM", atom
3675 read (card(18:20),'(a3)') res
3676 if ((atom(1:2).eq.'NA').or.(atom(1:2).eq.'CL').or.&
3677 (atom(1:2).eq.'CA').or.(atom(1:2).eq.'MG') &
3678 .or.(atom(1:2).eq.'K ')) &
3681 if (molecule.ne.5) molecprev=molecule
3683 nres_molec(molecule)=nres_molec(molecule)+1
3684 print *,"HERE",nres_molec(molecule)
3686 itype(ires,molecule)=rescode(ires,res,0,molecule)
3687 read(card(31:54),'(3f8.3)') (c(j,ires),j=1,3)
3691 10 write (iout,'(a,i5)') ' Number of residues found: ',ires
3692 if (ires.eq.0) return
3693 ! Calculate dummy residue coordinates inside the "chain" of a multichain
3696 if (((ires_old.ne.ires).and.(molecule.ne.5)) &
3698 nres_molec(molecule)=nres_molec(molecule)-2
3699 print *,'I have',nres, nres_molec(:)
3701 do k=1,4 ! ions are without dummy
3702 if (nres_molec(k).eq.0) cycle
3704 ! write (iout,*) i,itype(i,1)
3705 ! if (itype(i,1).eq.ntyp1) then
3706 ! write (iout,*) "dummy",i,itype(i,1)
3708 ! c(j,i)=((c(j,i-1)+c(j,i+1))/2+2*c(j,i-1)-c(j,i-2))/2
3709 ! c(j,i)=(c(j,i-1)+c(j,i+1))/2
3713 if (itype(i,k).eq.ntyp1_molec(k)) then
3714 if (itype(i+1,k).eq.ntyp1_molec(k)) then
3715 if (itype(i+2,k).eq.0) then
3716 ! print *,"masz sieczke"
3718 if (itype(i+2,j).ne.0) then
3720 itype(i+1,j)=ntyp1_molec(j)
3721 nres_molec(k)=nres_molec(k)-1
3722 nres_molec(j)=nres_molec(j)+1
3728 ! 16/01/2014 by Adasko: Adding to dummy atoms in the chain
3729 ! first is connected prevous chain (itype(i+1,1).eq.ntyp1)=true
3730 ! second dummy atom is conected to next chain itype(i+1,1).eq.ntyp1=false
3731 ! if (unres_pdb) then
3732 ! 2/15/2013 by Adam: corrected insertion of the last dummy residue
3733 ! print *,i,'tu dochodze'
3734 ! call refsys(i-3,i-2,i-1,e1,e2,e3,fail)
3742 ! c(j,i)=c(j,i-1)-1.9d0*e2(j)
3746 dcj=(c(j,i-2)-c(j,i-3))/2.0
3747 if (dcj.eq.0) dcj=1.23591524223
3752 else !itype(i+1,1).eq.ntyp1
3753 ! if (unres_pdb) then
3754 ! 2/15/2013 by Adam: corrected insertion of the first dummy residue
3755 ! call refsys(i+1,i+2,i+3,e1,e2,e3,fail)
3762 ! c(j,i)=c(j,i+1)-1.9d0*e2(j)
3763 c(j,i)=c(j,i-1)+1.9d0*(-e1(j)+e2(j))/sqrt(2.0d0)
3767 dcj=(c(j,i+3)-c(j,i+2))/2.0
3768 if (dcj.eq.0) dcj=1.23591524223
3773 endif !itype(i+1,1).eq.ntyp1
3774 endif !itype.eq.ntyp1
3778 ! Calculate the CM of the last side chain.
3782 dc(j,ires)=sccor(j,iii)
3785 call sccenter(ires,iii,sccor)
3791 ! print *,"molecule",molecule
3792 if ((itype(nres,1).ne.10)) then
3794 if (molecule.eq.5) molecule=molecprev
3795 itype(nres,molecule)=ntyp1_molec(molecule)
3796 nres_molec(molecule)=nres_molec(molecule)+1
3797 ! if (unres_pdb) then
3798 ! 2/15/2013 by Adam: corrected insertion of the last dummy residue
3799 ! call refsys(nres-3,nres-2,nres-1,e1,e2,e3,fail)
3806 ! c(j,nres)=c(j,nres-1)-1.9d0*e2(j)
3810 dcj=(c(j,nres-2)-c(j,nres-3))/2.0
3811 c(j,nres)=c(j,nres-1)+dcj
3812 c(j,2*nres)=c(j,nres)
3816 ! print *,'I have',nres, nres_molec(:)
3818 !el kontrola nres w pliku inputowym WHAM-a w porownaniu z wartoscia wczytana z pliku pdb
3820 if (nres.ne.nres0) then
3821 write (iout,*) "Error: wrong parameter value: NRES=",nres,&
3823 stop "Error nres value in WHAM input"
3826 !---------------------------------
3827 !el reallocate tables
3830 ! hfrag_alloc(j,i)=hfrag(j,i)
3833 ! bfrag_alloc(j,i)=bfrag(j,i)
3839 ! allocate(hfrag(2,nres/3)) !(2,maxres/3)
3840 !el allocate(hfrag(2,nhfrag)) !(2,maxres/3)
3841 !el allocate(bfrag(4,nbfrag)) !(4,maxres/3)
3842 ! allocate(bfrag(4,nres/3)) !(4,maxres/3)
3846 ! hfrag(j,i)=hfrag_alloc(j,i)
3851 ! bfrag(j,i)=bfrag_alloc(j,i)
3854 !el end reallocate tables
3855 !---------------------------------
3863 c(j,2*nres)=c(j,nres)
3866 if (itype(1,1).eq.ntyp1) then
3870 ! 2/15/2013 by Adam: corrected insertion of the first dummy residue
3871 call refsys(2,3,4,e1,e2,e3,fail)
3878 ! c(j,1)=c(j,2)-1.9d0*e2(j)
3879 c(j,1)=c(j,2)+1.9d0*(e1(j)-e2(j))/sqrt(2.0d0)
3883 dcj=(c(j,4)-c(j,3))/2.0
3889 ! First lets assign correct dummy to correct type of chain
3891 if (itype(1,1).eq.ntyp1) then
3892 if (itype(2,1).eq.0) then
3894 if (itype(2,j).ne.0) then
3896 itype(1,j)=ntyp1_molec(j)
3897 nres_molec(1)=nres_molec(1)-1
3898 nres_molec(j)=nres_molec(j)+1
3905 print *,'I have',nres, nres_molec(:)
3907 ! Copy the coordinates to reference coordinates
3913 ! Calculate internal coordinates.
3915 write (iout,'(/a)') &
3916 "Cartesian coordinates of the reference structure"
3917 write (iout,'(a,16x,3(3x,a5),5x,3(3x,a5))') &
3918 "Residue","X(CA)","Y(CA)","Z(CA)","X(SC)","Y(SC)","Z(SC)"
3920 write (iout,'(5(a3,1x),i5,3f8.3,5x,3f8.3)') &
3921 (restyp(itype(ires,j),j),j=1,5),ires,(c(j,ires),j=1,3),&
3922 (c(j,ires+nres),j=1,3)
3925 ! znamy już nres wiec mozna alokowac tablice
3926 ! Calculate internal coordinates.
3927 if(me.eq.king.or..not.out1file)then
3928 write (iout,'(a)') &
3929 "Backbone and SC coordinates as read from the PDB"
3931 write (iout,'(i5,i3,2x,a,3f8.3,5x,3f8.3)') &
3932 ires,itype(ires,1),restyp(itype(ires,1),1),(c(j,ires),j=1,3),&
3933 (c(j,nres+ires),j=1,3)
3936 ! NOW LETS ROCK! SORTING
3937 allocate(c_temporary(3,2*nres))
3938 allocate(itype_temporary(nres,5))
3939 if (.not.allocated(molnum)) allocate(molnum(nres+1))
3940 if (.not.allocated(istype)) write(iout,*) &
3941 "SOMETHING WRONG WITH ISTYTPE"
3942 allocate(istype_temp(nres))
3943 itype_temporary(:,:)=0
3947 if (itype(i,k).ne.0) then
3949 c_temporary(j,seqalingbegin)=c(j,i)
3950 c_temporary(j,seqalingbegin+nres)=c(j,i+nres)
3953 itype_temporary(seqalingbegin,k)=itype(i,k)
3954 print *,i,k,itype(i,k),itype_temporary(seqalingbegin,k),seqalingbegin
3955 istype_temp(seqalingbegin)=istype(i)
3956 molnum(seqalingbegin)=k
3957 seqalingbegin=seqalingbegin+1
3963 c(j,i)=c_temporary(j,i)
3968 itype(i,k)=itype_temporary(i,k)
3969 istype(i)=istype_temp(i)
3972 ! if (itype(1,1).eq.ntyp1) then
3975 ! if (unres_pdb) then
3976 ! 2/15/2013 by Adam: corrected insertion of the first dummy residue
3977 ! call refsys(2,3,4,e1,e2,e3,fail)
3984 ! c(j,1)=c(j,2)-1.9d0*e2(j)
3988 ! dcj=(c(j,4)-c(j,3))/2.0
3990 ! c(j,nres+1)=c(j,1)
3996 write (iout,'(/a)') &
3997 "Cartesian coordinates of the reference structure after sorting"
3998 write (iout,'(a,16x,3(3x,a5),5x,3(3x,a5))') &
3999 "Residue","X(CA)","Y(CA)","Z(CA)","X(SC)","Y(SC)","Z(SC)"
4001 write (iout,'(5(a3,1x),i5,3f8.3,5x,3f8.3)') &
4002 (restyp(itype(ires,j),j),j=1,5),ires,(c(j,ires),j=1,3),&
4003 (c(j,ires+nres),j=1,3)
4007 ! print *,seqalingbegin,nres
4008 if(.not.allocated(vbld)) then
4009 allocate(vbld(2*nres))
4014 if(.not.allocated(vbld_inv)) then
4015 allocate(vbld_inv(2*nres))
4021 if(.not.allocated(theta)) then
4022 allocate(theta(nres+2))
4026 if(.not.allocated(phi)) allocate(phi(nres+2))
4027 if(.not.allocated(alph)) allocate(alph(nres+2))
4028 if(.not.allocated(omeg)) allocate(omeg(nres+2))
4029 if(.not.allocated(thetaref)) allocate(thetaref(nres+2))
4030 if(.not.allocated(phiref)) allocate(phiref(nres+2))
4031 if(.not.allocated(costtab)) allocate(costtab(nres))
4032 if(.not.allocated(sinttab)) allocate(sinttab(nres))
4033 if(.not.allocated(cost2tab)) allocate(cost2tab(nres))
4034 if(.not.allocated(sint2tab)) allocate(sint2tab(nres))
4035 if(.not.allocated(xxref)) allocate(xxref(nres))
4036 if(.not.allocated(yyref)) allocate(yyref(nres))
4037 if(.not.allocated(zzref)) allocate(zzref(nres)) !(maxres)
4038 if(.not.allocated(dc_norm)) then
4039 ! if(.not.allocated(dc_norm)) allocate(dc_norm(3,0:2*nres+2))
4040 allocate(dc_norm(3,0:2*nres+2))
4044 call int_from_cart(.true.,.false.)
4045 call sc_loc_geom(.false.)
4047 thetaref(i)=theta(i)
4057 dc(j,i)=c(j,i+1)-c(j,i)
4058 dc_norm(j,i)=dc(j,i)*vbld_inv(i+1)
4063 dc(j,i+nres)=c(j,i+nres)-c(j,i)
4064 dc_norm(j,i+nres)=dc(j,i+nres)*vbld_inv(i+nres)
4066 ! write (iout,*) i,(dc(j,i+nres),j=1,3),(dc_norm(j,i+nres),j=1,3),&
4070 ! Copy the coordinates to reference coordinates
4071 ! Splits to single chain if occurs
4075 ! cref(j,i,cou)=c(j,i)
4079 if(.not.allocated(cref)) allocate(cref(3,2*nres+2,maxperm)) !(3,maxres2+2,maxperm)
4080 if(.not.allocated(chain_rep)) allocate(chain_rep(3,2*nres+2,maxsym)) !(3,maxres2+2,maxsym)
4081 if(.not.allocated(tabperm)) allocate(tabperm(maxperm,maxsym)) !(maxperm,maxsym)
4082 !-----------------------------
4086 write (iout,*) "symetr", symetr
4089 ! write (iout,*) "spraw lancuchy",(c(j,i),j=1,3)
4091 if ((itype(i-1,1).eq.ntyp1).and.(i.gt.2)) then
4094 ! write (iout,*) "spraw lancuchy",(c(j,i),j=1,3)
4099 cref(j,i,cou)=c(j,i)
4100 cref(j,i+nres,cou)=c(j,i+nres)
4102 chain_rep(j,lll,kkk)=c(j,i)
4103 chain_rep(j,lll+nres,kkk)=c(j,i+nres)
4107 write (iout,*) chain_length
4108 if (chain_length.eq.0) chain_length=nres
4110 chain_rep(j,chain_length,symetr)=chain_rep(j,chain_length,1)
4111 chain_rep(j,chain_length+nres,symetr) &
4112 =chain_rep(j,chain_length+nres,1)
4115 ! write (iout,*) "spraw lancuchy",chain_length,symetr
4117 ! do kkk=1,chain_length
4118 ! write (iout,*) itype(kkk,1),(chain_rep(j,kkk,i), j=1,3)
4122 ! makes copy of chains
4123 write (iout,*) "symetr", symetr
4128 if (symetr.gt.1) then
4135 write(iout,*) (tabperm(i,kkk),kkk=1,4)
4141 write (iout,*) i,icha
4142 do lll=1,chain_length
4144 if (cou.le.nres) then
4146 kupa=mod(lll,chain_length)
4147 iprzes=(kkk-1)*chain_length+lll
4148 if (kupa.eq.0) kupa=chain_length
4149 write (iout,*) "kupa", kupa
4150 cref(j,iprzes,i)=chain_rep(j,kupa,icha)
4151 cref(j,iprzes+nres,i)=chain_rep(j,kupa+nres,icha)
4158 !-koniec robienia kopii
4161 write (iout,*) "nowa struktura", nperm
4163 write (iout,110) restyp(itype(i,1),1),i,cref(1,i,kkk),&
4165 cref(3,i,kkk),cref(1,nres+i,kkk),&
4166 cref(2,nres+i,kkk),cref(3,nres+i,kkk)
4168 100 format (//' alpha-carbon coordinates ',&
4169 ' centroid coordinates'/ &
4170 ' ', 6X,'X',11X,'Y',11X,'Z', &
4171 10X,'X',11X,'Y',11X,'Z')
4172 110 format (a,'(',i5,')',6f12.5)
4178 bfrag(i,j)=bfrag(i,j)-ishift
4184 hfrag(i,j)=hfrag(i,j)-ishift
4190 end subroutine readpdb
4191 #if .not. defined(WHAM_RUN) && .not. defined(CLUSTER)
4192 !-----------------------------------------------------------------------------
4194 !-----------------------------------------------------------------------------
4195 subroutine read_control
4209 use random, only: random_init
4210 ! implicit real*8 (a-h,o-z)
4211 ! include 'DIMENSIONS'
4213 use prng, only:prng_restart
4215 logical :: OKRandom!, prng_restart
4218 ! include 'COMMON.IOUNITS'
4219 ! include 'COMMON.TIME1'
4220 ! include 'COMMON.THREAD'
4221 ! include 'COMMON.SBRIDGE'
4222 ! include 'COMMON.CONTROL'
4223 ! include 'COMMON.MCM'
4224 ! include 'COMMON.MAP'
4225 ! include 'COMMON.HEADER'
4226 ! include 'COMMON.CSA'
4227 ! include 'COMMON.CHAIN'
4228 ! include 'COMMON.MUCA'
4229 ! include 'COMMON.MD'
4230 ! include 'COMMON.FFIELD'
4231 ! include 'COMMON.INTERACT'
4232 ! include 'COMMON.SETUP'
4233 !el integer :: KDIAG,ICORFL,IXDR
4234 !el COMMON /MACHSW/ KDIAG,ICORFL,IXDR
4235 character(len=8),dimension(0:3) :: diagmeth = reshape((/'Library ',&
4236 'EVVRSP ','Givens ','Jacobi '/),shape(diagmeth))
4237 ! character(len=80) :: ucase
4238 character(len=640) :: controlcard
4240 real(kind=8) :: seed,rmsdbc,rmsdbc1max,rmsdbcm,drms,timem!,&
4246 read (INP,'(a)') titel
4247 call card_concat(controlcard,.true.)
4248 ! out1file=index(controlcard,'OUT1FILE').gt.0 .or. fg_rank.gt.0
4249 ! print *,"Processor",me," fg_rank",fg_rank," out1file",out1file
4250 call reada(controlcard,'SEED',seed,0.0D0)
4251 call random_init(seed)
4252 ! Set up the time limit (caution! The time must be input in minutes!)
4253 read_cart=index(controlcard,'READ_CART').gt.0
4254 call readi(controlcard,'CONSTR_DIST',constr_dist,0)
4255 call readi(controlcard,'SYM',symetr,1)
4256 call reada(controlcard,'TIMLIM',timlim,960.0D0) ! default 16 hours
4257 unres_pdb = index(controlcard,'UNRES_PDB') .gt. 0
4258 call reada(controlcard,'SAFETY',safety,30.0D0) ! default 30 minutes
4259 call reada(controlcard,'RMSDBC',rmsdbc,3.0D0)
4260 call reada(controlcard,'RMSDBC1',rmsdbc1,0.5D0)
4261 call reada(controlcard,'RMSDBC1MAX',rmsdbc1max,1.5D0)
4262 call reada(controlcard,'RMSDBCM',rmsdbcm,3.0D0)
4263 call reada(controlcard,'DRMS',drms,0.1D0)
4264 if(me.eq.king .or. .not. out1file .and. fg_rank.eq.0) then
4265 write (iout,'(a,f10.1)')'RMSDBC = ',rmsdbc
4266 write (iout,'(a,f10.1)')'RMSDBC1 = ',rmsdbc1
4267 write (iout,'(a,f10.1)')'RMSDBC1MAX = ',rmsdbc1max
4268 write (iout,'(a,f10.1)')'DRMS = ',drms
4269 write (iout,'(a,f10.1)')'RMSDBCM = ',rmsdbcm
4270 write (iout,'(a,f10.1)') 'Time limit (min):',timlim
4272 call readi(controlcard,'NZ_START',nz_start,0)
4273 call readi(controlcard,'NZ_END',nz_end,0)
4274 call readi(controlcard,'IZ_SC',iz_sc,0)
4275 timlim=60.0D0*timlim
4276 safety = 60.0d0*safety
4279 call reada(controlcard,"T_BATH",t_bath,300.0d0)
4280 !C SHIELD keyword sets if the shielding effect of side-chains is used
4281 !C 0 denots no shielding is used all peptide are equally despite the
4282 !C solvent accesible area
4283 !C 1 the newly introduced function
4284 !C 2 reseved for further possible developement
4285 call readi(controlcard,'SHIELD',shield_mode,0)
4286 !C if(me.eq.king .or. .not. out1file .and. fg_rank.eq.0) then
4287 write(iout,*) "shield_mode",shield_mode
4288 call readi(controlcard,'TORMODE',tor_mode,0)
4289 !C if(me.eq.king .or. .not. out1file .and. fg_rank.eq.0) then
4290 write(iout,*) "torsional and valence angle mode",tor_mode
4292 !C Varibles set size of box
4293 with_theta_constr = index(controlcard,"WITH_THETA_CONSTR").gt.0
4294 protein=index(controlcard,"PROTEIN").gt.0
4295 ions=index(controlcard,"IONS").gt.0
4296 nucleic=index(controlcard,"NUCLEIC").gt.0
4297 write (iout,*) "with_theta_constr ",with_theta_constr
4298 AFMlog=(index(controlcard,'AFM'))
4299 selfguide=(index(controlcard,'SELFGUIDE'))
4300 print *,'AFMlog',AFMlog,selfguide,"KUPA"
4301 call readi(controlcard,'GENCONSTR',genconstr,0)
4302 call reada(controlcard,'BOXX',boxxsize,100.0d0)
4303 call reada(controlcard,'BOXY',boxysize,100.0d0)
4304 call reada(controlcard,'BOXZ',boxzsize,100.0d0)
4305 call readi(controlcard,'TUBEMOD',tubemode,0)
4306 print *,"SCELE",scelemode
4307 call readi(controlcard,"SCELEMODE",scelemode,0)
4308 print *,"SCELE",scelemode
4310 ! elemode = 0 is orignal UNRES electrostatics
4311 ! elemode = 1 is "Momo" potentials in progress
4312 ! elemode = 2 is in development EVALD
4315 write (iout,*) TUBEmode,"TUBEMODE"
4316 if (TUBEmode.gt.0) then
4317 call reada(controlcard,"XTUBE",tubecenter(1),0.0d0)
4318 call reada(controlcard,"YTUBE",tubecenter(2),0.0d0)
4319 call reada(controlcard,"ZTUBE",tubecenter(3),0.0d0)
4320 call reada(controlcard,"RTUBE",tubeR0,0.0d0)
4321 call reada(controlcard,"TUBETOP",bordtubetop,boxzsize)
4322 call reada(controlcard,"TUBEBOT",bordtubebot,0.0d0)
4323 call reada(controlcard,"TUBEBUF",tubebufthick,1.0d0)
4324 buftubebot=bordtubebot+tubebufthick
4325 buftubetop=bordtubetop-tubebufthick
4328 ! CUTOFFF ON ELECTROSTATICS
4329 call reada(controlcard,"R_CUT_ELE",r_cut_ele,15.0d0)
4330 call reada(controlcard,"LAMBDA_ELE",rlamb_ele,0.3d0)
4331 write(iout,*) "R_CUT_ELE=",r_cut_ele
4332 ! Lipidic parameters
4333 call reada(controlcard,"LIPTHICK",lipthick,0.0d0)
4334 call reada(controlcard,"LIPAQBUF",lipbufthick,0.0d0)
4335 if (lipthick.gt.0.0d0) then
4336 bordliptop=(boxzsize+lipthick)/2.0
4337 bordlipbot=bordliptop-lipthick
4338 if ((bordliptop.gt.boxzsize).or.(bordlipbot.lt.0.0)) &
4339 write(iout,*) "WARNING WRONG SIZE OF LIPIDIC PHASE"
4340 buflipbot=bordlipbot+lipbufthick
4341 bufliptop=bordliptop-lipbufthick
4342 if ((lipbufthick*2.0d0).gt.lipthick) &
4343 write(iout,*) "WARNING WRONG SIZE OF LIP AQ BUF"
4344 endif !lipthick.gt.0
4345 write(iout,*) "bordliptop=",bordliptop
4346 write(iout,*) "bordlipbot=",bordlipbot
4347 write(iout,*) "bufliptop=",bufliptop
4348 write(iout,*) "buflipbot=",buflipbot
4349 write (iout,*) "SHIELD MODE",shield_mode
4351 !C-------------------------
4352 minim=(index(controlcard,'MINIMIZE').gt.0)
4353 dccart=(index(controlcard,'CART').gt.0)
4354 overlapsc=(index(controlcard,'OVERLAP').gt.0)
4355 overlapsc=.not.overlapsc
4356 searchsc=(index(controlcard,'NOSEARCHSC').gt.0)
4357 searchsc=.not.searchsc
4358 sideadd=(index(controlcard,'SIDEADD').gt.0)
4359 energy_dec=(index(controlcard,'ENERGY_DEC').gt.0)
4360 outpdb=(index(controlcard,'PDBOUT').gt.0)
4361 outmol2=(index(controlcard,'MOL2OUT').gt.0)
4362 pdbref=(index(controlcard,'PDBREF').gt.0)
4363 refstr=pdbref .or. (index(controlcard,'REFSTR').gt.0)
4364 indpdb=index(controlcard,'PDBSTART')
4365 extconf=(index(controlcard,'EXTCONF').gt.0)
4366 call readi(controlcard,'IPRINT',iprint,0)
4367 call readi(controlcard,'MAXGEN',maxgen,10000)
4368 call readi(controlcard,'MAXOVERLAP',maxoverlap,1000)
4369 call readi(controlcard,"KDIAG",kdiag,0)
4370 call readi(controlcard,"RESCALE_MODE",rescale_mode,2)
4371 if(me.eq.king .or. .not. out1file .and. fg_rank.eq.0) &
4372 write (iout,*) "RESCALE_MODE",rescale_mode
4373 split_ene=index(controlcard,'SPLIT_ENE').gt.0
4374 if (index(controlcard,'REGULAR').gt.0.0D0) then
4375 call reada(controlcard,'WEIDIS',weidis,0.1D0)
4379 if (index(controlcard,'CHECKGRAD').gt.0) then
4381 if (index(controlcard,'CART').gt.0) then
4383 elseif (index(controlcard,'CARINT').gt.0) then
4388 elseif (index(controlcard,'THREAD').gt.0) then
4390 call readi(controlcard,'THREAD',nthread,0)
4391 if (nthread.gt.0) then
4392 call reada(controlcard,'WEIDIS',weidis,0.1D0)
4395 write (iout,'(a)')'A number has to follow the THREAD keyword.'
4396 stop 'Error termination in Read_Control.'
4398 else if (index(controlcard,'MCMA').gt.0) then
4400 else if (index(controlcard,'MCEE').gt.0) then
4402 else if (index(controlcard,'MULTCONF').gt.0) then
4404 else if (index(controlcard,'MAP').gt.0) then
4406 call readi(controlcard,'MAP',nmap,0)
4407 else if (index(controlcard,'CSA').gt.0) then
4409 !rc else if (index(controlcard,'ZSCORE').gt.0) then
4411 !rc ZSCORE is rm from UNRES, modecalc=9 is available
4414 !fcm else if (index(controlcard,'MCMF').gt.0) then
4416 else if (index(controlcard,'SOFTREG').gt.0) then
4418 else if (index(controlcard,'CHECK_BOND').gt.0) then
4420 else if (index(controlcard,'TEST').gt.0) then
4422 else if (index(controlcard,'MD').gt.0) then
4424 else if (index(controlcard,'RE ').gt.0) then
4428 lmuca=index(controlcard,'MUCA').gt.0
4429 call readi(controlcard,'MUCADYN',mucadyn,0)
4430 call readi(controlcard,'MUCASMOOTH',muca_smooth,0)
4431 if (lmuca .and. (me.eq.king .or. .not.out1file )) &
4433 write (iout,*) 'MUCADYN=',mucadyn
4434 write (iout,*) 'MUCASMOOTH=',muca_smooth
4437 iscode=index(controlcard,'ONE_LETTER')
4438 indphi=index(controlcard,'PHI')
4439 indback=index(controlcard,'BACK')
4440 iranconf=index(controlcard,'RAND_CONF')
4441 i2ndstr=index(controlcard,'USE_SEC_PRED')
4442 gradout=index(controlcard,'GRADOUT').gt.0
4443 gnorm_check=index(controlcard,'GNORM_CHECK').gt.0
4444 call reada(controlcard,'DISTCHAINMAX',distchainmax,5.0d0)
4445 if (me.eq.king .or. .not.out1file ) &
4446 write (iout,*) "DISTCHAINMAX",distchainmax
4448 if(me.eq.king.or..not.out1file) &
4449 write (iout,'(2a)') diagmeth(kdiag),&
4450 ' routine used to diagonalize matrices.'
4451 if (shield_mode.gt.0) then
4452 pi=4.0D0*datan(1.0D0)
4453 !C VSolvSphere the volume of solving sphere
4455 !C rpp(1,1) is the energy r0 for peptide group contact and will be used for it
4456 !C there will be no distinction between proline peptide group and normal peptide
4457 !C group in case of shielding parameters
4458 VSolvSphere=4.0/3.0*pi*(4.50d0)**3
4459 VSolvSphere_div=VSolvSphere-4.0/3.0*pi*(4.50/2.0)**3
4460 write (iout,*) VSolvSphere,VSolvSphere_div
4461 !C long axis of side chain
4463 ! long_r_sidechain(i)=vbldsc0(1,i)
4464 ! short_r_sidechain(i)=sigma0(i)
4465 ! write(iout,*) "parame for long and short axis",i,vbldsc0(1,i),&
4471 end subroutine read_control
4472 !-----------------------------------------------------------------------------
4473 subroutine read_REMDpar
4475 ! Read REMD settings
4482 use control_data, only:out1file
4483 ! implicit real*8 (a-h,o-z)
4484 ! include 'DIMENSIONS'
4485 ! include 'COMMON.IOUNITS'
4486 ! include 'COMMON.TIME1'
4487 ! include 'COMMON.MD'
4490 !el include 'COMMON.LANGEVIN'
4492 !el include 'COMMON.LANGEVIN.lang0'
4494 ! include 'COMMON.INTERACT'
4495 ! include 'COMMON.NAMES'
4496 ! include 'COMMON.GEO'
4497 ! include 'COMMON.REMD'
4498 ! include 'COMMON.CONTROL'
4499 ! include 'COMMON.SETUP'
4500 ! character(len=80) :: ucase
4501 character(len=320) :: controlcard
4502 character(len=3200) :: controlcard1
4503 integer :: iremd_m_total
4506 ! real(kind=8) :: var,ene
4508 if(me.eq.king.or..not.out1file) &
4509 write (iout,*) "REMD setup"
4511 call card_concat(controlcard,.true.)
4512 call readi(controlcard,"NREP",nrep,3)
4513 call readi(controlcard,"NSTEX",nstex,1000)
4514 call reada(controlcard,"RETMIN",retmin,10.0d0)
4515 call reada(controlcard,"RETMAX",retmax,1000.0d0)
4516 mremdsync=(index(controlcard,'SYNC').gt.0)
4517 call readi(controlcard,"NSYN",i_sync_step,100)
4518 restart1file=(index(controlcard,'REST1FILE').gt.0)
4519 traj1file=(index(controlcard,'TRAJ1FILE').gt.0)
4520 call readi(controlcard,"TRAJCACHE",max_cache_traj_use,1)
4521 if(max_cache_traj_use.gt.max_cache_traj) &
4522 max_cache_traj_use=max_cache_traj
4523 if(me.eq.king.or..not.out1file) then
4524 !d if (traj1file) then
4525 !rc caching is in testing - NTWX is not ignored
4526 !d write (iout,*) "NTWX value is ignored"
4527 !d write (iout,*) " trajectory is stored to one file by master"
4528 !d write (iout,*) " before exchange at NSTEX intervals"
4530 write (iout,*) "NREP= ",nrep
4531 write (iout,*) "NSTEX= ",nstex
4532 write (iout,*) "SYNC= ",mremdsync
4533 write (iout,*) "NSYN= ",i_sync_step
4534 write (iout,*) "TRAJCACHE= ",max_cache_traj_use
4537 allocate(remd_t(nrep),remd_m(nrep)) !(maxprocs)
4538 if (index(controlcard,'TLIST').gt.0) then
4540 call card_concat(controlcard1,.true.)
4541 read(controlcard1,*) (remd_t(i),i=1,nrep)
4542 if(me.eq.king.or..not.out1file) &
4543 write (iout,*)'tlist',(remd_t(i),i=1,nrep)
4546 if (index(controlcard,'MLIST').gt.0) then
4548 call card_concat(controlcard1,.true.)
4549 read(controlcard1,*) (remd_m(i),i=1,nrep)
4550 if(me.eq.king.or..not.out1file) then
4551 write (iout,*)'mlist',(remd_m(i),i=1,nrep)
4554 iremd_m_total=iremd_m_total+remd_m(i)
4556 write (iout,*) 'Total number of replicas ',iremd_m_total
4559 if(me.eq.king.or..not.out1file) &
4560 write (iout,'(/30(1h=),a,29(1h=)/)') " End of REMD run setup "
4562 end subroutine read_REMDpar
4563 !-----------------------------------------------------------------------------
4564 subroutine read_MDpar
4568 use control_data, only: r_cut,rlamb,out1file
4570 use geometry_data, only: pi
4572 ! implicit real*8 (a-h,o-z)
4573 ! include 'DIMENSIONS'
4574 ! include 'COMMON.IOUNITS'
4575 ! include 'COMMON.TIME1'
4576 ! include 'COMMON.MD'
4579 !el include 'COMMON.LANGEVIN'
4581 !el include 'COMMON.LANGEVIN.lang0'
4583 ! include 'COMMON.INTERACT'
4584 ! include 'COMMON.NAMES'
4585 ! include 'COMMON.GEO'
4586 ! include 'COMMON.SETUP'
4587 ! include 'COMMON.CONTROL'
4588 ! include 'COMMON.SPLITELE'
4589 ! character(len=80) :: ucase
4590 character(len=320) :: controlcard
4595 call card_concat(controlcard,.true.)
4596 call readi(controlcard,"NSTEP",n_timestep,1000000)
4597 call readi(controlcard,"NTWE",ntwe,100)
4598 call readi(controlcard,"NTWX",ntwx,1000)
4599 call reada(controlcard,"DT",d_time,1.0d-1)
4600 call reada(controlcard,"DVMAX",dvmax,2.0d1)
4601 call reada(controlcard,"DAMAX",damax,1.0d1)
4602 call reada(controlcard,"EDRIFTMAX",edriftmax,1.0d+1)
4603 call readi(controlcard,"LANG",lang,0)
4604 RESPA = index(controlcard,"RESPA") .gt. 0
4605 call readi(controlcard,"NTIME_SPLIT",ntime_split,1)
4606 ntime_split0=ntime_split
4607 call readi(controlcard,"MAXTIME_SPLIT",maxtime_split,64)
4608 ntime_split0=ntime_split
4609 call reada(controlcard,"R_CUT",r_cut,2.0d0)
4610 call reada(controlcard,"LAMBDA",rlamb,0.3d0)
4611 rest = index(controlcard,"REST").gt.0
4612 tbf = index(controlcard,"TBF").gt.0
4613 usampl = index(controlcard,"USAMPL").gt.0
4614 mdpdb = index(controlcard,"MDPDB").gt.0
4615 call reada(controlcard,"T_BATH",t_bath,300.0d0)
4616 call reada(controlcard,"TAU_BATH",tau_bath,1.0d-1)
4617 call reada(controlcard,"EQ_TIME",eq_time,1.0d+4)
4618 call readi(controlcard,"RESET_MOMENT",count_reset_moment,1000)
4619 if (count_reset_moment.eq.0) count_reset_moment=1000000000
4620 call readi(controlcard,"RESET_VEL",count_reset_vel,1000)
4621 reset_moment=lang.eq.0 .and. tbf .and. count_reset_moment.gt.0
4622 reset_vel=lang.eq.0 .and. tbf .and. count_reset_vel.gt.0
4623 if (count_reset_vel.eq.0) count_reset_vel=1000000000
4624 large = index(controlcard,"LARGE").gt.0
4625 print_compon = index(controlcard,"PRINT_COMPON").gt.0
4626 rattle = index(controlcard,"RATTLE").gt.0
4627 preminim=(index(controlcard,'PREMINIM').gt.0)
4628 write (iout,*) "PREMINIM ",preminim
4629 dccart=(index(controlcard,'CART').gt.0)
4630 if (preminim) call read_minim
4631 ! if performing umbrella sampling, fragments constrained are read from the fragment file
4637 if(me.eq.king.or..not.out1file) then
4639 write (iout,'(27(1h=),a26,27(1h=))') " Parameters of the MD run "
4641 write (iout,'(a)') "The units are:"
4642 write (iout,'(a)') "positions: angstrom, time: 48.9 fs"
4643 write (iout,'(2a)') "velocity: angstrom/(48.9 fs),",&
4644 " acceleration: angstrom/(48.9 fs)**2"
4645 write (iout,'(a)') "energy: kcal/mol, temperature: K"
4647 write (iout,'(a60,i10)') "Number of time steps:",n_timestep
4648 write (iout,'(a60,f10.5,a)') &
4649 "Initial time step of numerical integration:",d_time,&
4651 write (iout,'(60x,f10.5,a)') d_time*48.9," fs"
4653 write (iout,'(2a,i4,a)') &
4654 "A-MTS algorithm used; initial time step for fast-varying",&
4655 " short-range forces split into",ntime_split," steps."
4656 write (iout,'(a,f5.2,a,f5.2)') "Short-range force cutoff",&
4657 r_cut," lambda",rlamb
4659 write (iout,'(2a,f10.5)') &
4660 "Maximum acceleration threshold to reduce the time step",&
4661 "/increase split number:",damax
4662 write (iout,'(2a,f10.5)') &
4663 "Maximum predicted energy drift to reduce the timestep",&
4664 "/increase split number:",edriftmax
4665 write (iout,'(a60,f10.5)') &
4666 "Maximum velocity threshold to reduce velocities:",dvmax
4667 write (iout,'(a60,i10)') "Frequency of property output:",ntwe
4668 write (iout,'(a60,i10)') "Frequency of coordinate output:",ntwx
4669 if (rattle) write (iout,'(a60)') &
4670 "Rattle algorithm used to constrain the virtual bonds"
4674 call reada(controlcard,"ETAWAT",etawat,0.8904d0)
4675 call reada(controlcard,"RWAT",rwat,1.4d0)
4676 call reada(controlcard,"SCAL_FRIC",scal_fric,2.0d-2)
4677 surfarea=index(controlcard,"SURFAREA").gt.0
4678 call readi(controlcard,"RESET_FRICMAT",reset_fricmat,1000)
4679 if(me.eq.king.or..not.out1file)then
4680 write (iout,'(/a,$)') "Langevin dynamics calculation"
4682 write (iout,'(a/)') &
4683 " with direct integration of Langevin equations"
4684 else if (lang.eq.2) then
4685 write (iout,'(a/)') " with TINKER stochasic MD integrator"
4686 else if (lang.eq.3) then
4687 write (iout,'(a/)') " with Ciccotti's stochasic MD integrator"
4688 else if (lang.eq.4) then
4689 write (iout,'(a/)') " in overdamped mode"
4691 write (iout,'(//a,i5)') &
4692 "=========== ERROR: Unknown Langevin dynamics mode:",lang
4695 write (iout,'(a60,f10.5)') "Temperature:",t_bath
4696 write (iout,'(a60,f10.5)') "Viscosity of the solvent:",etawat
4697 write (iout,'(a60,f10.5)') "Radius of solvent molecule:",rwat
4698 write (iout,'(a60,f10.5)') &
4699 "Scaling factor of the friction forces:",scal_fric
4700 if (surfarea) write (iout,'(2a,i10,a)') &
4701 "Friction coefficients will be scaled by solvent-accessible",&
4702 " surface area every",reset_fricmat," steps."
4704 ! Calculate friction coefficients and bounds of stochastic forces
4705 eta=6*pi*cPoise*etawat
4706 if(me.eq.king.or..not.out1file) &
4707 write(iout,'(a60,f10.5)')"Eta of the solvent in natural units:",&
4710 do j=1,5 !types of molecules
4711 gamp(j)=scal_fric*(pstok(j)+rwat)*eta
4712 stdfp(j)=dsqrt(2*Rb*t_bath/d_time)
4714 allocate(gamsc(ntyp1,5),stdfsc(ntyp1,5)) !(ntyp1)
4715 do j=1,5 !types of molecules
4717 gamsc(i,j)=scal_fric*(restok(i,j)+rwat)*eta
4718 stdfsc(i,j)=dsqrt(2*Rb*t_bath/d_time)
4722 if(me.eq.king.or..not.out1file)then
4723 write (iout,'(/2a/)') &
4724 "Radii of site types and friction coefficients and std's of",&
4725 " stochastic forces of fully exposed sites"
4726 write (iout,'(a5,f5.2,2f10.5)')'p',pstok,gamp(1),stdfp*dsqrt(gamp(1))
4728 write (iout,'(a5,f5.2,2f10.5)') restyp(i,1),restok(i,1),&
4729 gamsc(i,1),stdfsc(i,1)*dsqrt(gamsc(i,1))
4733 if(me.eq.king.or..not.out1file)then
4734 write (iout,'(a)') "Berendsen bath calculation"
4735 write (iout,'(a60,f10.5)') "Temperature:",t_bath
4736 write (iout,'(a60,f10.5)') "Coupling constant (tau):",tau_bath
4738 write (iout,'(a,i10,a)') "Momenta will be reset at zero every",&
4739 count_reset_moment," steps"
4741 write (iout,'(a,i10,a)') &
4742 "Velocities will be reset at random every",count_reset_vel,&
4746 if(me.eq.king.or..not.out1file) &
4747 write (iout,'(a31)') "Microcanonical mode calculation"
4749 if(me.eq.king.or..not.out1file)then
4750 if (rest) write (iout,'(/a/)') "===== Calculation restarted ===="
4752 write(iout,*) "MD running with constraints."
4753 write(iout,*) "Equilibration time ", eq_time, " mtus."
4754 write(iout,*) "Constraining ", nfrag," fragments."
4755 write(iout,*) "Length of each fragment, weight and q0:"
4757 write (iout,*) "Set of restraints #",iset
4759 write(iout,'(2i5,f8.1,f7.4)') ifrag(1,i,iset),&
4760 ifrag(2,i,iset),wfrag(i,iset),qinfrag(i,iset)
4762 write(iout,*) "constraints between ", npair, "fragments."
4763 write(iout,*) "constraint pairs, weights and q0:"
4765 write(iout,'(2i5,f8.1,f7.4)') ipair(1,i,iset),&
4766 ipair(2,i,iset),wpair(i,iset),qinpair(i,iset)
4768 write(iout,*) "angle constraints within ", nfrag_back,&
4769 "backbone fragments."
4770 write(iout,*) "fragment, weights:"
4772 write(iout,'(2i5,3f8.1)') ifrag_back(1,i,iset),&
4773 ifrag_back(2,i,iset),wfrag_back(1,i,iset),&
4774 wfrag_back(2,i,iset),wfrag_back(3,i,iset)
4777 iset=mod(kolor,nset)+1
4780 if(me.eq.king.or..not.out1file) &
4781 write (iout,'(/30(1h=),a,29(1h=)/)') " End of MD run setup "
4783 end subroutine read_MDpar
4784 !-----------------------------------------------------------------------------
4788 ! implicit real*8 (a-h,o-z)
4789 ! include 'DIMENSIONS'
4790 ! include 'COMMON.MAP'
4791 ! include 'COMMON.IOUNITS'
4792 character(len=3) :: angid(4) = (/'THE','PHI','ALP','OME'/)
4793 character(len=80) :: mapcard !,ucase
4796 ! real(kind=8) :: var,ene
4799 read (inp,'(a)') mapcard
4800 mapcard=ucase(mapcard)
4801 if (index(mapcard,'PHI').gt.0) then
4803 else if (index(mapcard,'THE').gt.0) then
4805 else if (index(mapcard,'ALP').gt.0) then
4807 else if (index(mapcard,'OME').gt.0) then
4810 write(iout,'(a)')'Error - illegal variable spec in MAP card.'
4811 stop 'Error - illegal variable spec in MAP card.'
4813 call readi (mapcard,'RES1',res1(imap),0)
4814 call readi (mapcard,'RES2',res2(imap),0)
4815 if (res1(imap).eq.0) then
4816 res1(imap)=res2(imap)
4817 else if (res2(imap).eq.0) then
4818 res2(imap)=res1(imap)
4820 if(res1(imap)*res2(imap).eq.0 .or. res1(imap).gt.res2(imap))then
4821 write (iout,'(a)') &
4822 'Error - illegal definition of variable group in MAP.'
4823 stop 'Error - illegal definition of variable group in MAP.'
4825 call reada(mapcard,'FROM',ang_from(imap),0.0D0)
4826 call reada(mapcard,'TO',ang_to(imap),0.0D0)
4827 call readi(mapcard,'NSTEP',nstep(imap),0)
4828 if (ang_from(imap).eq.ang_to(imap) .or. nstep(imap).eq.0) then
4829 write (iout,'(a)') &
4830 'Illegal boundary and/or step size specification in MAP.'
4831 stop 'Illegal boundary and/or step size specification in MAP.'
4835 end subroutine map_read
4836 !-----------------------------------------------------------------------------
4839 use control_data, only: vdisulf
4841 ! implicit real*8 (a-h,o-z)
4842 ! include 'DIMENSIONS'
4843 ! include 'COMMON.IOUNITS'
4844 ! include 'COMMON.GEO'
4845 ! include 'COMMON.CSA'
4846 ! include 'COMMON.BANK'
4847 ! include 'COMMON.CONTROL'
4848 ! character(len=80) :: ucase
4849 character(len=620) :: mcmcard
4851 ! integer :: ntf,ik,iw_pdb
4852 ! real(kind=8) :: var,ene
4854 call card_concat(mcmcard,.true.)
4856 call readi(mcmcard,'NCONF',nconf,50)
4857 call readi(mcmcard,'NADD',nadd,0)
4858 call readi(mcmcard,'JSTART',jstart,1)
4859 call readi(mcmcard,'JEND',jend,1)
4860 call readi(mcmcard,'NSTMAX',nstmax,500000)
4861 call readi(mcmcard,'N0',n0,1)
4862 call readi(mcmcard,'N1',n1,6)
4863 call readi(mcmcard,'N2',n2,4)
4864 call readi(mcmcard,'N3',n3,0)
4865 call readi(mcmcard,'N4',n4,0)
4866 call readi(mcmcard,'N5',n5,0)
4867 call readi(mcmcard,'N6',n6,10)
4868 call readi(mcmcard,'N7',n7,0)
4869 call readi(mcmcard,'N8',n8,0)
4870 call readi(mcmcard,'N9',n9,0)
4871 call readi(mcmcard,'N14',n14,0)
4872 call readi(mcmcard,'N15',n15,0)
4873 call readi(mcmcard,'N16',n16,0)
4874 call readi(mcmcard,'N17',n17,0)
4875 call readi(mcmcard,'N18',n18,0)
4877 vdisulf=(index(mcmcard,'DYNSS').gt.0)
4879 call readi(mcmcard,'NDIFF',ndiff,2)
4880 call reada(mcmcard,'DIFFCUT',diffcut,0.0d0)
4881 call readi(mcmcard,'IS1',is1,1)
4882 call readi(mcmcard,'IS2',is2,8)
4883 call readi(mcmcard,'NRAN0',nran0,4)
4884 call readi(mcmcard,'NRAN1',nran1,2)
4885 call readi(mcmcard,'IRR',irr,1)
4886 call readi(mcmcard,'NSEED',nseed,20)
4887 call readi(mcmcard,'NTOTAL',ntotal,10000)
4888 call reada(mcmcard,'CUT1',cut1,2.0d0)
4889 call reada(mcmcard,'CUT2',cut2,5.0d0)
4890 call reada(mcmcard,'ESTOP',estop,-3000.0d0)
4891 call readi(mcmcard,'ICMAX',icmax,3)
4892 call readi(mcmcard,'IRESTART',irestart,0)
4893 !!bankt call readi(mcmcard,'NBANKTM',ntbankm,0)
4896 call reada(mcmcard,'DELE',dele,20.0d0)
4897 call reada(mcmcard,'DIFCUT',difcut,720.0d0)
4898 call readi(mcmcard,'IREF',iref,0)
4899 call reada(mcmcard,'RMSCUT',rmscut,4.0d0)
4900 call reada(mcmcard,'PNCCUT',pnccut,0.5d0)
4901 call readi(mcmcard,'NCONF_IN',nconf_in,0)
4902 call reada(mcmcard,'RDIH_BIAS',rdih_bias,0.5d0)
4903 write (iout,*) "NCONF_IN",nconf_in
4905 end subroutine csaread
4906 !-----------------------------------------------------------------------------
4910 use control_data, only: MaxMoveType
4913 ! implicit real*8 (a-h,o-z)
4914 ! include 'DIMENSIONS'
4915 ! include 'COMMON.MCM'
4916 ! include 'COMMON.MCE'
4917 ! include 'COMMON.IOUNITS'
4918 ! character(len=80) :: ucase
4919 character(len=320) :: mcmcard
4922 ! real(kind=8) :: var,ene
4924 call card_concat(mcmcard,.true.)
4925 call readi(mcmcard,'MAXACC',maxacc,100)
4926 call readi(mcmcard,'MAX_MCM_IT',max_mcm_it,10000)
4927 call readi(mcmcard,'MAXTRIAL',maxtrial,100)
4928 call readi(mcmcard,'MAXTRIAL_ITER',maxtrial_iter,1000)
4929 call readi(mcmcard,'MAXREPM',maxrepm,200)
4930 call reada(mcmcard,'RANFRACT',RanFract,0.5D0)
4931 call reada(mcmcard,'POOL_FRACT',pool_fraction,0.01D0)
4932 call reada(mcmcard,'OVERLAP',overlap_cut,1.0D3)
4933 call reada(mcmcard,'E_UP',e_up,5.0D0)
4934 call reada(mcmcard,'DELTE',delte,0.1D0)
4935 call readi(mcmcard,'NSWEEP',nsweep,5)
4936 call readi(mcmcard,'NSTEPH',nsteph,0)
4937 call readi(mcmcard,'NSTEPC',nstepc,0)
4938 call reada(mcmcard,'TMIN',tmin,298.0D0)
4939 call reada(mcmcard,'TMAX',tmax,298.0D0)
4940 call readi(mcmcard,'NWINDOW',nwindow,0)
4941 call readi(mcmcard,'PRINT_MC',print_mc,0)
4942 print_stat=(index(mcmcard,'NO_PRINT_STAT').le.0)
4943 print_int=(index(mcmcard,'NO_PRINT_INT').le.0)
4944 ent_read=(index(mcmcard,'ENT_READ').gt.0)
4945 call readi(mcmcard,'SAVE_FREQ',save_frequency,1000)
4946 call readi(mcmcard,'MESSAGE_FREQ',message_frequency,1000)
4947 call readi(mcmcard,'POOL_READ_FREQ',pool_read_freq,5000)
4948 call readi(mcmcard,'POOL_SAVE_FREQ',pool_save_freq,1000)
4949 call readi(mcmcard,'PRINT_FREQ',print_freq,1000)
4950 if (nwindow.gt.0) then
4951 allocate(winstart(nwindow)) !!el (maxres)
4952 allocate(winend(nwindow)) !!el
4953 allocate(winlen(nwindow)) !!el
4954 read (inp,*) (winstart(i),winend(i),i=1,nwindow)
4956 winlen(i)=winend(i)-winstart(i)+1
4959 if (tmax.lt.tmin) tmax=tmin
4960 if (tmax.eq.tmin) then
4964 if (nstepc.gt.0 .and. nsteph.gt.0) then
4965 tsteph=(tmax/tmin)**(1.0D0/(nsteph+0.0D0))
4966 tstepc=(tmax/tmin)**(1.0D0/(nstepc+0.0D0))
4968 allocate(sumpro_type(0:MaxMoveType)) !(0:MaxMoveType)
4969 ! Probabilities of different move types
4970 sumpro_type(0)=0.0D0
4971 call reada(mcmcard,'MULTI_BOND',sumpro_type(1),1.0d0)
4972 call reada(mcmcard,'ONE_ANGLE' ,sumpro_type(2),2.0d0)
4973 sumpro_type(2)=sumpro_type(1)+sumpro_type(2)
4974 call reada(mcmcard,'THETA' ,sumpro_type(3),0.0d0)
4975 sumpro_type(3)=sumpro_type(2)+sumpro_type(3)
4976 call reada(mcmcard,'SIDE_CHAIN',sumpro_type(4),0.5d0)
4977 sumpro_type(4)=sumpro_type(3)+sumpro_type(4)
4979 print *,'i',i,' sumprotype',sumpro_type(i)
4980 sumpro_type(i)=sumpro_type(i)/sumpro_type(MaxMoveType)
4981 print *,'i',i,' sumprotype',sumpro_type(i)
4984 end subroutine mcmread
4985 !-----------------------------------------------------------------------------
4986 subroutine read_minim
4989 ! implicit real*8 (a-h,o-z)
4990 ! include 'DIMENSIONS'
4991 ! include 'COMMON.MINIM'
4992 ! include 'COMMON.IOUNITS'
4993 ! character(len=80) :: ucase
4994 character(len=320) :: minimcard
4996 ! integer :: ntf,ik,iw_pdb
4997 ! real(kind=8) :: var,ene
4999 call card_concat(minimcard,.true.)
5000 call readi(minimcard,'MAXMIN',maxmin,2000)
5001 call readi(minimcard,'MAXFUN',maxfun,5000)
5002 call readi(minimcard,'MINMIN',minmin,maxmin)
5003 call readi(minimcard,'MINFUN',minfun,maxmin)
5004 call reada(minimcard,'TOLF',tolf,1.0D-2)
5005 call reada(minimcard,'RTOLF',rtolf,1.0D-4)
5006 print_min_stat=min0(index(minimcard,'PRINT_MIN_STAT'),1)
5007 print_min_res=min0(index(minimcard,'PRINT_MIN_RES'),1)
5008 print_min_ini=min0(index(minimcard,'PRINT_MIN_INI'),1)
5009 write (iout,'(/80(1h*)/20x,a/80(1h*))') &
5010 'Options in energy minimization:'
5011 write (iout,'(4(a,i5),a,1pe14.5,a,1pe14.5)') &
5012 'MaxMin:',MaxMin,' MaxFun:',MaxFun,&
5013 'MinMin:',MinMin,' MinFun:',MinFun,&
5014 ' TolF:',TolF,' RTolF:',RTolF
5016 end subroutine read_minim
5017 !-----------------------------------------------------------------------------
5018 subroutine openunits
5020 use MD_data, only: usampl
5023 use control_data, only:out1file
5024 use control, only: getenv_loc
5025 ! implicit real*8 (a-h,o-z)
5026 ! include 'DIMENSIONS'
5029 character(len=16) :: form,nodename
5030 integer :: nodelen,ierror,npos
5032 ! include 'COMMON.SETUP'
5033 ! include 'COMMON.IOUNITS'
5034 ! include 'COMMON.MD'
5035 ! include 'COMMON.CONTROL'
5036 integer :: lenpre,lenpot,lentmp !,ilen
5038 character(len=3) :: out1file_text !,ucase
5039 character(len=3) :: ll
5042 ! integer :: ntf,ik,iw_pdb
5043 ! real(kind=8) :: var,ene
5045 ! print *,"Processor",myrank,"fg_rank",fg_rank," entered openunits"
5046 call getenv_loc("PREFIX",prefix)
5048 call getenv_loc("POT",pot)
5049 call getenv_loc("DIRTMP",tmpdir)
5050 call getenv_loc("CURDIR",curdir)
5051 call getenv_loc("OUT1FILE",out1file_text)
5052 ! print *,"Processor",myrank,"fg_rank",fg_rank," did GETENV"
5053 out1file_text=ucase(out1file_text)
5054 if (out1file_text(1:1).eq."Y") then
5057 out1file=fg_rank.gt.0
5062 if (lentmp.gt.0) then
5063 write (*,'(80(1h!))')
5064 write (*,'(a,19x,a,19x,a)') "!"," A T T E N T I O N ","!"
5065 write (*,'(80(1h!))')
5066 write (*,*)"All output files will be on node /tmp directory."
5068 call MPI_GET_PROCESSOR_NAME( nodename, nodelen, IERROR )
5069 if (me.eq.king) then
5070 write (*,*) "The master node is ",nodename
5071 else if (fg_rank.eq.0) then
5072 write (*,*) "I am the CG slave node ",nodename
5074 write (*,*) "I am the FG slave node ",nodename
5077 PREFIX = tmpdir(:lentmp)//'/'//prefix(:lenpre)
5078 lenpre = lentmp+lenpre+1
5080 entname=prefix(:lenpre)//'_'//pot(:lenpot)//'.entr'
5081 ! Get the names and open the input files
5082 #if defined(WINIFL) || defined(WINPGI)
5083 open(1,file=pref_orig(:ilen(pref_orig))// &
5084 '.inp',status='old',readonly,shared)
5085 open (9,file=prefix(:ilen(prefix))//'.intin',status='unknown')
5086 ! open (18,file=prefix(:ilen(prefix))//'.entin',status='unknown')
5087 ! Get parameter filenames and open the parameter files.
5088 call getenv_loc('BONDPAR',bondname)
5089 open (ibond,file=bondname,status='old',readonly,shared)
5090 call getenv_loc('BONDPAR_NUCL',bondname_nucl)
5091 open (ibond_nucl,file=bondname_nucl,status='old',readonly,shared)
5092 call getenv_loc('THETPAR',thetname)
5093 open (ithep,file=thetname,status='old',readonly,shared)
5094 call getenv_loc('ROTPAR',rotname)
5095 open (irotam,file=rotname,status='old',readonly,shared)
5096 call getenv_loc('TORPAR',torname)
5097 open (itorp,file=torname,status='old',readonly,shared)
5098 call getenv_loc('TORDPAR',tordname)
5099 open (itordp,file=tordname,status='old',readonly,shared)
5100 call getenv_loc('FOURIER',fouriername)
5101 open (ifourier,file=fouriername,status='old',readonly,shared)
5102 call getenv_loc('ELEPAR',elename)
5103 open (ielep,file=elename,status='old',readonly,shared)
5104 call getenv_loc('SIDEPAR',sidename)
5105 open (isidep,file=sidename,status='old',readonly,shared)
5107 call getenv_loc('THETPAR_NUCL',thetname_nucl)
5108 open (ithep_nucl,file=thetname_nucl,status='old',readonly,shared)
5109 call getenv_loc('ROTPAR_NUCL',rotname_nucl)
5110 open (irotam_nucl,file=rotname_nucl,status='old',readonly,shared)
5111 call getenv_loc('TORPAR_NUCL',torname_nucl)
5112 open (itorp_nucl,file=torname_nucl,status='old',readonly,shared)
5113 call getenv_loc('TORDPAR_NUCL',tordname_nucl)
5114 open (itordp_nucl,file=tordname_nucl,status='old',readonly,shared)
5115 call getenv_loc('SIDEPAR_NUCL',sidename_nucl)
5116 open (isidep_nucl,file=sidename_nucl,status='old',readonly,shared)
5119 #elif (defined CRAY) || (defined AIX)
5120 open(1,file=pref_orig(:ilen(pref_orig))//'.inp',status='old',&
5122 ! print *,"Processor",myrank," opened file 1"
5123 open (9,file=prefix(:ilen(prefix))//'.intin',status='unknown')
5124 ! print *,"Processor",myrank," opened file 9"
5125 ! open (18,file=prefix(:ilen(prefix))//'.entin',status='unknown')
5126 ! Get parameter filenames and open the parameter files.
5127 call getenv_loc('BONDPAR',bondname)
5128 open (ibond,file=bondname,status='old',action='read')
5129 call getenv_loc('BONDPAR_NUCL',bondname_nucl)
5130 open (ibond_nucl,file=bondname_nucl,status='old',action='read')
5132 ! print *,"Processor",myrank," opened file IBOND"
5133 call getenv_loc('THETPAR',thetname)
5134 open (ithep,file=thetname,status='old',action='read')
5135 ! print *,"Processor",myrank," opened file ITHEP"
5136 call getenv_loc('ROTPAR',rotname)
5137 open (irotam,file=rotname,status='old',action='read')
5138 ! print *,"Processor",myrank," opened file IROTAM"
5139 call getenv_loc('TORPAR',torname)
5140 open (itorp,file=torname,status='old',action='read')
5141 ! print *,"Processor",myrank," opened file ITORP"
5142 call getenv_loc('TORDPAR',tordname)
5143 open (itordp,file=tordname,status='old',action='read')
5144 ! print *,"Processor",myrank," opened file ITORDP"
5145 call getenv_loc('SCCORPAR',sccorname)
5146 open (isccor,file=sccorname,status='old',action='read')
5147 ! print *,"Processor",myrank," opened file ISCCOR"
5148 call getenv_loc('FOURIER',fouriername)
5149 open (ifourier,file=fouriername,status='old',action='read')
5150 ! print *,"Processor",myrank," opened file IFOURIER"
5151 call getenv_loc('ELEPAR',elename)
5152 open (ielep,file=elename,status='old',action='read')
5153 ! print *,"Processor",myrank," opened file IELEP"
5154 call getenv_loc('SIDEPAR',sidename)
5155 open (isidep,file=sidename,status='old',action='read')
5157 call getenv_loc('THETPAR_NUCL',thetname_nucl)
5158 open (ithep_nucl,file=thetname_nucl,status='old',action='read')
5159 call getenv_loc('ROTPAR_NUCL',rotname_nucl)
5160 open (irotam_nucl,file=rotname_nucl,status='old',action='read')
5161 call getenv_loc('TORPAR_NUCL',torname_nucl)
5162 open (itorp_nucl,file=torname_nucl,status='old',action='read')
5163 call getenv_loc('TORDPAR_NUCL',tordname_nucl)
5164 open (itordp_nucl,file=tordname_nucl,status='old',action='read')
5165 call getenv_loc('SIDEPAR_NUCL',sidename_nucl)
5166 open (isidep_nucl,file=sidename_nucl,status='old',action='read')
5168 call getenv_loc('LIPTRANPAR',liptranname)
5169 open (iliptranpar,file=liptranname,status='old',action='read')
5170 call getenv_loc('TUBEPAR',tubename)
5171 open (itube,file=tubename,status='old',action='read')
5172 call getenv_loc('IONPAR',ionname)
5173 open (iion,file=ionname,status='old',action='read')
5175 ! print *,"Processor",myrank," opened file ISIDEP"
5176 ! print *,"Processor",myrank," opened parameter files"
5178 open(1,file=pref_orig(:ilen(pref_orig))//'.inp',status='old')
5179 open (9,file=prefix(:ilen(prefix))//'.intin',status='unknown')
5180 ! open (18,file=prefix(:ilen(prefix))//'.entin',status='unknown')
5181 ! Get parameter filenames and open the parameter files.
5182 call getenv_loc('BONDPAR',bondname)
5183 open (ibond,file=bondname,status='old')
5184 call getenv_loc('BONDPAR_NUCL',bondname_nucl)
5185 open (ibond_nucl,file=bondname_nucl,status='old')
5187 call getenv_loc('THETPAR',thetname)
5188 open (ithep,file=thetname,status='old')
5189 call getenv_loc('ROTPAR',rotname)
5190 open (irotam,file=rotname,status='old')
5191 call getenv_loc('TORPAR',torname)
5192 open (itorp,file=torname,status='old')
5193 call getenv_loc('TORDPAR',tordname)
5194 open (itordp,file=tordname,status='old')
5195 call getenv_loc('SCCORPAR',sccorname)
5196 open (isccor,file=sccorname,status='old')
5197 call getenv_loc('FOURIER',fouriername)
5198 open (ifourier,file=fouriername,status='old')
5199 call getenv_loc('ELEPAR',elename)
5200 open (ielep,file=elename,status='old')
5201 call getenv_loc('SIDEPAR',sidename)
5202 open (isidep,file=sidename,status='old')
5204 open (ithep_nucl,file=thetname_nucl,status='old')
5205 call getenv_loc('ROTPAR_NUCL',rotname_nucl)
5206 open (irotam_nucl,file=rotname_nucl,status='old')
5207 call getenv_loc('TORPAR_NUCL',torname_nucl)
5208 open (itorp_nucl,file=torname_nucl,status='old')
5209 call getenv_loc('TORDPAR_NUCL',tordname_nucl)
5210 open (itordp_nucl,file=tordname_nucl,status='old')
5211 call getenv_loc('SIDEPAR_NUCL',sidename_nucl)
5212 open (isidep_nucl,file=sidename_nucl,status='old')
5214 call getenv_loc('LIPTRANPAR',liptranname)
5215 open (iliptranpar,file=liptranname,status='old')
5216 call getenv_loc('TUBEPAR',tubename)
5217 open (itube,file=tubename,status='old')
5218 call getenv_loc('IONPAR',ionname)
5219 open (iion,file=ionname,status='old')
5221 open(1,file=pref_orig(:ilen(pref_orig))//'.inp',status='old',&
5223 open (9,file=prefix(:ilen(prefix))//'.intin',status='unknown')
5224 ! open (18,file=prefix(:ilen(prefix))//'.entin',status='unknown')
5225 ! Get parameter filenames and open the parameter files.
5226 call getenv_loc('BONDPAR',bondname)
5227 open (ibond,file=bondname,status='old',action='read')
5228 call getenv_loc('BONDPAR_NUCL',bondname_nucl)
5229 open (ibond_nucl,file=bondname_nucl,status='old',action='read')
5230 call getenv_loc('THETPAR',thetname)
5231 open (ithep,file=thetname,status='old',action='read')
5232 call getenv_loc('ROTPAR',rotname)
5233 open (irotam,file=rotname,status='old',action='read')
5234 call getenv_loc('TORPAR',torname)
5235 open (itorp,file=torname,status='old',action='read')
5236 call getenv_loc('TORDPAR',tordname)
5237 open (itordp,file=tordname,status='old',action='read')
5238 call getenv_loc('SCCORPAR',sccorname)
5239 open (isccor,file=sccorname,status='old',action='read')
5241 call getenv_loc('THETPARPDB',thetname_pdb)
5242 print *,"thetname_pdb ",thetname_pdb
5243 open (ithep_pdb,file=thetname_pdb,status='old',action='read')
5244 print *,ithep_pdb," opened"
5246 call getenv_loc('FOURIER',fouriername)
5247 open (ifourier,file=fouriername,status='old',readonly)
5248 call getenv_loc('ELEPAR',elename)
5249 open (ielep,file=elename,status='old',readonly)
5250 call getenv_loc('SIDEPAR',sidename)
5251 open (isidep,file=sidename,status='old',readonly)
5253 call getenv_loc('THETPAR_NUCL',thetname_nucl)
5254 open (ithep_nucl,file=thetname_nucl,status='old',action='read')
5255 call getenv_loc('ROTPAR_NUCL',rotname_nucl)
5256 open (irotam_nucl,file=rotname_nucl,status='old',action='read')
5257 call getenv_loc('TORPAR_NUCL',torname_nucl)
5258 open (itorp_nucl,file=torname_nucl,status='old',action='read')
5259 call getenv_loc('TORDPAR_NUCL',tordname_nucl)
5260 open (itordp_nucl,file=tordname_nucl,status='old',action='read')
5261 call getenv_loc('SIDEPAR_NUCL',sidename_nucl)
5262 open (isidep_nucl,file=sidename_nucl,status='old',action='read')
5263 call getenv_loc('SIDEPAR_SCBASE',sidename_scbase)
5264 open (isidep_scbase,file=sidename_scbase,status='old',action='read')
5265 call getenv_loc('PEPPAR_PEPBASE',pepname_pepbase)
5266 open (isidep_pepbase,file=pepname_pepbase,status='old',action='read')
5267 call getenv_loc('SCPAR_PHOSPH',pepname_scpho)
5268 open (isidep_scpho,file=pepname_scpho,status='old',action='read')
5269 call getenv_loc('PEPPAR_PHOSPH',pepname_peppho)
5270 open (isidep_peppho,file=pepname_peppho,status='old',action='read')
5273 call getenv_loc('LIPTRANPAR',liptranname)
5274 open (iliptranpar,file=liptranname,status='old',action='read')
5275 call getenv_loc('TUBEPAR',tubename)
5276 open (itube,file=tubename,status='old',action='read')
5277 call getenv_loc('IONPAR',ionname)
5278 open (iion,file=ionname,status='old',action='read')
5281 call getenv_loc('ROTPARPDB',rotname_pdb)
5282 open (irotam_pdb,file=rotname_pdb,status='old',action='read')
5285 call getenv_loc('SCPPAR_NUCL',scpname_nucl)
5286 #if defined(WINIFL) || defined(WINPGI)
5287 open (iscpp_nucl,file=scpname_nucl,status='old',readonly,shared)
5288 #elif (defined CRAY) || (defined AIX)
5289 open (iscpp_nucl,file=scpname_nucl,status='old',action='read')
5291 open (iscpp_nucl,file=scpname_nucl,status='old')
5293 open (iscpp_nucl,file=scpname_nucl,status='old',action='read')
5298 ! 8/9/01 In the newest version SCp interaction constants are read from a file
5299 ! Use -DOLDSCP to use hard-coded constants instead.
5301 call getenv_loc('SCPPAR',scpname)
5302 #if defined(WINIFL) || defined(WINPGI)
5303 open (iscpp,file=scpname,status='old',readonly,shared)
5304 #elif (defined CRAY) || (defined AIX)
5305 open (iscpp,file=scpname,status='old',action='read')
5307 open (iscpp,file=scpname,status='old')
5309 open (iscpp,file=scpname,status='old',action='read')
5312 call getenv_loc('PATTERN',patname)
5313 #if defined(WINIFL) || defined(WINPGI)
5314 open (icbase,file=patname,status='old',readonly,shared)
5315 #elif (defined CRAY) || (defined AIX)
5316 open (icbase,file=patname,status='old',action='read')
5318 open (icbase,file=patname,status='old')
5320 open (icbase,file=patname,status='old',action='read')
5323 ! Open output file only for CG processes
5324 ! print *,"Processor",myrank," fg_rank",fg_rank
5325 if (fg_rank.eq.0) then
5327 if (nodes.eq.1) then
5330 npos = dlog10(dfloat(nodes-1))+1
5332 if (npos.lt.3) npos=3
5333 write (liczba,'(i1)') npos
5334 form = '(bz,i'//liczba(:ilen(liczba))//'.'//liczba(:ilen(liczba)) &
5336 write (liczba,form) me
5337 outname=prefix(:lenpre)//'.out_'//pot(:lenpot)// &
5338 liczba(:ilen(liczba))
5339 intname=prefix(:lenpre)//'_'//pot(:lenpot)//liczba(:ilen(liczba)) &
5341 pdbname=prefix(:lenpre)//'_'//pot(:lenpot)//liczba(:ilen(liczba)) &
5343 mol2name=prefix(:lenpre)//'_'//pot(:lenpot)// &
5344 liczba(:ilen(liczba))//'.mol2'
5345 statname=prefix(:lenpre)//'_'//pot(:lenpot)// &
5346 liczba(:ilen(liczba))//'.stat'
5348 call copy_to_tmp(pref_orig(:ilen(pref_orig))//'_'//pot(:lenpot) &
5349 //liczba(:ilen(liczba))//'.stat')
5350 rest2name=prefix(:ilen(prefix))//"_"//liczba(:ilen(liczba)) &
5353 qname=prefix(:lenpre)//'_'//pot(:lenpot)// &
5354 liczba(:ilen(liczba))//'.const'
5359 outname=prefix(:lenpre)//'.out_'//pot(:lenpot)
5360 intname=prefix(:lenpre)//'_'//pot(:lenpot)//'.int'
5361 pdbname=prefix(:lenpre)//'_'//pot(:lenpot)//'.pdb'
5362 mol2name=prefix(:lenpre)//'_'//pot(:lenpot)//'.mol2'
5363 statname=prefix(:lenpre)//'_'//pot(:lenpot)//'.stat'
5365 call copy_to_tmp(pref_orig(:ilen(pref_orig))//'_'//pot(:lenpot)// &
5367 rest2name=prefix(:ilen(prefix))//'.rst'
5369 qname=prefix(:lenpre)//'_'//pot(:lenpot)//'.const'
5372 #if defined(AIX) || defined(PGI)
5373 if (me.eq.king .or. .not. out1file) &
5374 open(iout,file=outname,status='unknown')
5376 if (fg_rank.gt.0) then
5377 write (liczba,'(i3.3)') myrank/nfgtasks
5378 write (ll,'(bz,i3.3)') fg_rank
5379 open(iout,file="debug"//liczba(:ilen(liczba))//"."//ll,&
5384 open(igeom,file=intname,status='unknown',position='append')
5385 open(ipdb,file=pdbname,status='unknown')
5386 open(imol2,file=mol2name,status='unknown')
5387 open(istat,file=statname,status='unknown',position='append')
5389 !1out open(iout,file=outname,status='unknown')
5392 if (me.eq.king .or. .not.out1file) &
5393 open(iout,file=outname,status='unknown')
5395 if (fg_rank.gt.0) then
5396 write (liczba,'(i3.3)') myrank/nfgtasks
5397 write (ll,'(bz,i3.3)') fg_rank
5398 open(iout,file="debug"//liczba(:ilen(liczba))//"."//ll,&
5403 open(igeom,file=intname,status='unknown',access='append')
5404 open(ipdb,file=pdbname,status='unknown')
5405 open(imol2,file=mol2name,status='unknown')
5406 open(istat,file=statname,status='unknown',access='append')
5408 !1out open(iout,file=outname,status='unknown')
5411 csa_rbank=prefix(:lenpre)//'.CSA.rbank'
5412 csa_seed=prefix(:lenpre)//'.CSA.seed'
5413 csa_history=prefix(:lenpre)//'.CSA.history'
5414 csa_bank=prefix(:lenpre)//'.CSA.bank'
5415 csa_bank1=prefix(:lenpre)//'.CSA.bank1'
5416 csa_alpha=prefix(:lenpre)//'.CSA.alpha'
5417 csa_alpha1=prefix(:lenpre)//'.CSA.alpha1'
5418 !!bankt csa_bankt=prefix(:lenpre)//'.CSA.bankt'
5419 csa_int=prefix(:lenpre)//'.int'
5420 csa_bank_reminimized=prefix(:lenpre)//'.CSA.bank_reminimized'
5421 csa_native_int=prefix(:lenpre)//'.CSA.native.int'
5422 csa_in=prefix(:lenpre)//'.CSA.in'
5423 ! print *,"Processor",myrank,"fg_rank",fg_rank," opened files"
5426 write (iout,'(80(1h-))')
5427 write (iout,'(30x,a)') "FILE ASSIGNMENT"
5428 write (iout,'(80(1h-))')
5429 write (iout,*) "Input file : ",&
5430 pref_orig(:ilen(pref_orig))//'.inp'
5431 write (iout,*) "Output file : ",&
5432 outname(:ilen(outname))
5434 write (iout,*) "Sidechain potential file : ",&
5435 sidename(:ilen(sidename))
5437 write (iout,*) "SCp potential file : ",&
5438 scpname(:ilen(scpname))
5440 write (iout,*) "Electrostatic potential file : ",&
5441 elename(:ilen(elename))
5442 write (iout,*) "Cumulant coefficient file : ",&
5443 fouriername(:ilen(fouriername))
5444 write (iout,*) "Torsional parameter file : ",&
5445 torname(:ilen(torname))
5446 write (iout,*) "Double torsional parameter file : ",&
5447 tordname(:ilen(tordname))
5448 write (iout,*) "SCCOR parameter file : ",&
5449 sccorname(:ilen(sccorname))
5450 write (iout,*) "Bond & inertia constant file : ",&
5451 bondname(:ilen(bondname))
5452 write (iout,*) "Bending parameter file : ",&
5453 thetname(:ilen(thetname))
5454 write (iout,*) "Rotamer parameter file : ",&
5455 rotname(:ilen(rotname))
5458 write (iout,*) "Thetpdb parameter file : ",&
5459 thetname_pdb(:ilen(thetname_pdb))
5462 write (iout,*) "Threading database : ",&
5463 patname(:ilen(patname))
5465 write (iout,*)" DIRTMP : ",&
5467 write (iout,'(80(1h-))')
5470 end subroutine openunits
5471 !-----------------------------------------------------------------------------
5474 use geometry_data, only: nres,dc
5476 ! implicit real*8 (a-h,o-z)
5477 ! include 'DIMENSIONS'
5478 ! include 'COMMON.CHAIN'
5479 ! include 'COMMON.IOUNITS'
5480 ! include 'COMMON.MD'
5483 ! real(kind=8) :: var,ene
5485 open(irest2,file=rest2name,status='unknown')
5486 read(irest2,*) totT,EK,potE,totE,t_bath
5489 ! AL 4/17/17: Now reading d_t(0,:) too
5491 read(irest2,'(3e15.5)') (d_t(j,i),j=1,3)
5494 ! AL 4/17/17: Now reading d_c(0,:) too
5496 read(irest2,'(3e15.5)') (dc(j,i),j=1,3)
5499 read (irest2,*) iset
5503 end subroutine readrst
5504 !-----------------------------------------------------------------------------
5505 subroutine read_fragments
5509 use control_data, only:out1file
5512 ! implicit real*8 (a-h,o-z)
5513 ! include 'DIMENSIONS'
5517 ! include 'COMMON.SETUP'
5518 ! include 'COMMON.CHAIN'
5519 ! include 'COMMON.IOUNITS'
5520 ! include 'COMMON.MD'
5521 ! include 'COMMON.CONTROL'
5524 ! real(kind=8) :: var,ene
5526 read(inp,*) nset,nfrag,npair,nfrag_back
5528 !el from module energy
5529 ! if(.not.allocated(mset)) allocate(mset(nset)) !(maxprocs/20)
5530 if(.not.allocated(wfrag_back)) then
5531 allocate(wfrag_back(3,nfrag_back,nset)) !(3,maxfrag_back,maxprocs/20)
5532 allocate(ifrag_back(3,nfrag_back,nset)) !(3,maxfrag_back,maxprocs/20)
5534 allocate(qinfrag(nfrag,nset),wfrag(nfrag,nset)) !(50,maxprocs/20)
5535 allocate(ifrag(2,nfrag,nset)) !(2,50,maxprocs/20)
5537 allocate(qinpair(npair,nset),wpair(npair,nset)) !(100,maxprocs/20)
5538 allocate(ipair(2,npair,nset)) !(2,100,maxprocs/20)
5541 if(me.eq.king.or..not.out1file) &
5542 write(iout,*) "nset",nset," nfrag",nfrag," npair",npair,&
5543 " nfrag_back",nfrag_back
5545 read(inp,*) mset(iset)
5547 read(inp,*) wfrag(i,iset),ifrag(1,i,iset),ifrag(2,i,iset),&
5549 if(me.eq.king.or..not.out1file) &
5550 write(iout,*) "R ",i,wfrag(i,iset),ifrag(1,i,iset),&
5551 ifrag(2,i,iset), qinfrag(i,iset)
5554 read(inp,*) wpair(i,iset),ipair(1,i,iset),ipair(2,i,iset),&
5556 if(me.eq.king.or..not.out1file) &
5557 write(iout,*) "R ",i,wpair(i,iset),ipair(1,i,iset),&
5558 ipair(2,i,iset), qinpair(i,iset)
5561 read(inp,*) wfrag_back(1,i,iset),wfrag_back(2,i,iset),&
5562 wfrag_back(3,i,iset),&
5563 ifrag_back(1,i,iset),ifrag_back(2,i,iset)
5564 if(me.eq.king.or..not.out1file) &
5565 write(iout,*) "A",i,wfrag_back(1,i,iset),wfrag_back(2,i,iset),&
5566 wfrag_back(3,i,iset),ifrag_back(1,i,iset),ifrag_back(2,i,iset)
5570 end subroutine read_fragments
5571 !-----------------------------------------------------------------------------
5573 !-----------------------------------------------------------------------------
5577 ! implicit real*8 (a-h,o-z)
5578 ! include 'DIMENSIONS'
5579 ! include 'COMMON.CSA'
5580 ! include 'COMMON.BANK'
5581 ! include 'COMMON.IOUNITS'
5583 ! integer :: ntf,ik,iw_pdb
5584 ! real(kind=8) :: var,ene
5586 open(icsa_in,file=csa_in,status="old",err=100)
5587 read(icsa_in,*) nconf
5588 read(icsa_in,*) jstart,jend
5589 read(icsa_in,*) nstmax
5590 read(icsa_in,*) n1,n2,n3,n4,n5,n6,n7,n8,is1,is2
5591 read(icsa_in,*) nran0,nran1,irr
5592 read(icsa_in,*) nseed
5593 read(icsa_in,*) ntotal,cut1,cut2
5594 read(icsa_in,*) estop
5595 read(icsa_in,*) icmax,irestart
5596 read(icsa_in,*) ntbankm,dele,difcut
5597 read(icsa_in,*) iref,rmscut,pnccut
5598 read(icsa_in,*) ndiff
5605 end subroutine csa_read
5606 !-----------------------------------------------------------------------------
5607 subroutine initial_write
5610 ! implicit real*8 (a-h,o-z)
5611 ! include 'DIMENSIONS'
5612 ! include 'COMMON.CSA'
5613 ! include 'COMMON.BANK'
5614 ! include 'COMMON.IOUNITS'
5616 ! integer :: ntf,ik,iw_pdb
5617 ! real(kind=8) :: var,ene
5619 open(icsa_seed,file=csa_seed,status="unknown")
5620 write(icsa_seed,*) "seed"
5622 #if defined(AIX) || defined(PGI)
5623 open(icsa_history,file=csa_history,status="unknown",&
5626 open(icsa_history,file=csa_history,status="unknown",&
5629 write(icsa_history,*) nconf
5630 write(icsa_history,*) jstart,jend
5631 write(icsa_history,*) nstmax
5632 write(icsa_history,*) n1,n2,n3,n4,n5,n6,n7,n8,is1,is2
5633 write(icsa_history,*) nran0,nran1,irr
5634 write(icsa_history,*) nseed
5635 write(icsa_history,*) ntotal,cut1,cut2
5636 write(icsa_history,*) estop
5637 write(icsa_history,*) icmax,irestart
5638 write(icsa_history,*) ntbankm,dele,difcut
5639 write(icsa_history,*) iref,rmscut,pnccut
5640 write(icsa_history,*) ndiff
5642 write(icsa_history,*)
5645 open(icsa_bank1,file=csa_bank1,status="unknown")
5646 write(icsa_bank1,*) 0
5650 end subroutine initial_write
5651 !-----------------------------------------------------------------------------
5652 subroutine restart_write
5655 ! implicit real*8 (a-h,o-z)
5656 ! include 'DIMENSIONS'
5657 ! include 'COMMON.IOUNITS'
5658 ! include 'COMMON.CSA'
5659 ! include 'COMMON.BANK'
5661 ! integer :: ntf,ik,iw_pdb
5662 ! real(kind=8) :: var,ene
5664 #if defined(AIX) || defined(PGI)
5665 open(icsa_history,file=csa_history,position="append")
5667 open(icsa_history,file=csa_history,access="append")
5669 write(icsa_history,*)
5670 write(icsa_history,*) "This is restart"
5671 write(icsa_history,*)
5672 write(icsa_history,*) nconf
5673 write(icsa_history,*) jstart,jend
5674 write(icsa_history,*) nstmax
5675 write(icsa_history,*) n1,n2,n3,n4,n5,n6,n7,n8,is1,is2
5676 write(icsa_history,*) nran0,nran1,irr
5677 write(icsa_history,*) nseed
5678 write(icsa_history,*) ntotal,cut1,cut2
5679 write(icsa_history,*) estop
5680 write(icsa_history,*) icmax,irestart
5681 write(icsa_history,*) ntbankm,dele,difcut
5682 write(icsa_history,*) iref,rmscut,pnccut
5683 write(icsa_history,*) ndiff
5684 write(icsa_history,*)
5685 write(icsa_history,*) "irestart is: ", irestart
5687 write(icsa_history,*)
5691 end subroutine restart_write
5692 !-----------------------------------------------------------------------------
5694 !-----------------------------------------------------------------------------
5695 subroutine write_pdb(npdb,titelloc,ee)
5697 ! implicit real*8 (a-h,o-z)
5698 ! include 'DIMENSIONS'
5699 ! include 'COMMON.IOUNITS'
5700 character(len=50) :: titelloc1
5701 character*(*) :: titelloc
5702 character(len=3) :: zahl
5703 character(len=5) :: liczba5
5705 integer :: npdb !,ilen
5709 ! real(kind=8) :: var,ene
5713 if (npdb.lt.1000) then
5714 call numstr(npdb,zahl)
5715 open(ipdb,file=prefix(:lenpre)//'@@'//zahl//'.pdb')
5717 if (npdb.lt.10000) then
5718 write(liczba5,'(i1,i4)') 0,npdb
5720 write(liczba5,'(i5)') npdb
5722 open(ipdb,file=prefix(:lenpre)//'@@'//liczba5//'.pdb')
5724 call pdbout(ee,titelloc1,ipdb)
5727 end subroutine write_pdb
5728 !-----------------------------------------------------------------------------
5730 !-----------------------------------------------------------------------------
5731 subroutine write_thread_summary
5732 ! Thread the sequence through a database of known structures
5733 use control_data, only: refstr
5735 use energy_data, only: n_ene_comp
5737 ! implicit real*8 (a-h,o-z)
5738 ! include 'DIMENSIONS'
5740 use MPI_data !include 'COMMON.INFO'
5743 ! include 'COMMON.CONTROL'
5744 ! include 'COMMON.CHAIN'
5745 ! include 'COMMON.DBASE'
5746 ! include 'COMMON.INTERACT'
5747 ! include 'COMMON.VAR'
5748 ! include 'COMMON.THREAD'
5749 ! include 'COMMON.FFIELD'
5750 ! include 'COMMON.SBRIDGE'
5751 ! include 'COMMON.HEADER'
5752 ! include 'COMMON.NAMES'
5753 ! include 'COMMON.IOUNITS'
5754 ! include 'COMMON.TIME1'
5756 integer,dimension(maxthread) :: ip
5757 real(kind=8),dimension(0:n_ene) :: energia
5759 integer :: i,j,ii,jj,ipj,ik,kk,ist
5760 real(kind=8) :: enet,etot,rmsnat,rms,frac,frac_nn
5762 write (iout,'(30x,a/)') &
5763 ' *********** Summary threading statistics ************'
5764 write (iout,'(a)') 'Initial energies:'
5765 write (iout,'(a4,2x,a12,14a14,3a8)') &
5766 'No','seq',(ename(print_order(i)),i=1,nprint_ene),'ETOT',&
5767 'RMSnat','NatCONT','NNCONT','RMS'
5768 ! Energy sort patterns
5773 enet=ener(n_ene-1,ip(i))
5776 if (ener(n_ene-1,ip(j)).lt.enet) then
5778 enet=ener(n_ene-1,ip(j))
5790 ist=nres_base(2,ii)+ipatt(2,i)
5792 energia(i)=ener0(kk,i)
5794 etot=ener0(n_ene_comp+1,i)
5795 rmsnat=ener0(n_ene_comp+2,i)
5796 rms=ener0(n_ene_comp+3,i)
5797 frac=ener0(n_ene_comp+4,i)
5798 frac_nn=ener0(n_ene_comp+5,i)
5801 write (iout,'(i4,2x,a8,i4,14(1pe14.5),0pf8.3,f8.5,f8.5,f8.3)') &
5802 i,str_nam(ii),ist+1,&
5803 (energia(print_order(kk)),kk=1,nprint_ene),&
5804 etot,rmsnat,frac,frac_nn,rms
5806 write (iout,'(i4,2x,a8,i4,14(1pe14.5),0pf8.3)') &
5807 i,str_nam(ii),ist+1,&
5808 (energia(print_order(kk)),kk=1,nprint_ene),etot
5811 write (iout,'(//a)') 'Final energies:'
5812 write (iout,'(a4,2x,a12,17a14,3a8)') &
5813 'No','seq',(ename(print_order(kk)),kk=1,nprint_ene),'ETOT',&
5814 'RMSnat','NatCONT','NNCONT','RMS'
5818 ist=nres_base(2,ii)+ipatt(2,i)
5820 energia(kk)=ener(kk,ik)
5822 etot=ener(n_ene_comp+1,i)
5823 rmsnat=ener(n_ene_comp+2,i)
5824 rms=ener(n_ene_comp+3,i)
5825 frac=ener(n_ene_comp+4,i)
5826 frac_nn=ener(n_ene_comp+5,i)
5827 write (iout,'(i4,2x,a8,i4,14(1pe14.5),0pf8.3,f8.5,f8.5,f8.3)') &
5828 i,str_nam(ii),ist+1,&
5829 (energia(print_order(kk)),kk=1,nprint_ene),&
5830 etot,rmsnat,frac,frac_nn,rms
5832 write (iout,'(/a/)') 'IEXAM array:'
5833 write (iout,'(i5)') nexcl
5835 write (iout,'(2i5)') iexam(1,i),iexam(2,i)
5837 write (iout,'(/a,1pe14.4/a,1pe14.4/)') &
5838 'Max. time for threading step ',max_time_for_thread,&
5839 'Average time for threading step: ',ave_time_for_thread
5841 end subroutine write_thread_summary
5842 !-----------------------------------------------------------------------------
5843 subroutine write_stat_thread(ithread,ipattern,ist)
5845 use energy_data, only: n_ene_comp
5847 ! implicit real*8 (a-h,o-z)
5848 ! include "DIMENSIONS"
5849 ! include "COMMON.CONTROL"
5850 ! include "COMMON.IOUNITS"
5851 ! include "COMMON.THREAD"
5852 ! include "COMMON.FFIELD"
5853 ! include "COMMON.DBASE"
5854 ! include "COMMON.NAMES"
5855 real(kind=8),dimension(0:n_ene) :: energia
5857 integer :: ithread,ipattern,ist,i
5858 real(kind=8) :: etot,rmsnat,rms,frac,frac_nn
5860 #if defined(AIX) || defined(PGI)
5861 open(istat,file=statname,position='append')
5863 open(istat,file=statname,access='append')
5866 energia(i)=ener(i,ithread)
5868 etot=ener(n_ene_comp+1,ithread)
5869 rmsnat=ener(n_ene_comp+2,ithread)
5870 rms=ener(n_ene_comp+3,ithread)
5871 frac=ener(n_ene_comp+4,ithread)
5872 frac_nn=ener(n_ene_comp+5,ithread)
5873 write (istat,'(i4,2x,a8,i4,14(1pe14.5),0pf8.3,f8.5,f8.5,f8.3)') &
5874 ithread,str_nam(ipattern),ist+1,&
5875 (energia(print_order(i)),i=1,nprint_ene),&
5876 etot,rmsnat,frac,frac_nn,rms
5879 end subroutine write_stat_thread
5880 !-----------------------------------------------------------------------------
5882 !-----------------------------------------------------------------------------
5883 end module io_config