1 subroutine read_control
8 include 'COMMON.IOUNITS'
10 include 'COMMON.SBRIDGE'
11 include 'COMMON.CONTROL'
12 include 'COMMON.CLUSTER'
13 include 'COMMON.CHAIN'
14 include 'COMMON.HEADER'
15 include 'COMMON.FFIELD'
17 character*320 controlcard,ucase
23 read (INP,'(a80)') titel
24 call card_concat(controlcard)
26 call readi(controlcard,'NRES',nres,0)
27 write (iout,*) "NRES",NRES
28 call readi(controlcard,'RESCALE',rescale_mode,2)
29 call readi(controlcard,'PDBOUT',outpdb,0)
30 call readi(controlcard,'MOL2OUT',outmol2,0)
31 refstr=(index(controlcard,'REFSTR').gt.0)
32 write (iout,*) "REFSTR",refstr
33 pdbref=(index(controlcard,'PDBREF').gt.0)
34 dyn_ss=(index(controlcard,'DYN_SS').gt.0)
35 iscode=index(controlcard,'ONE_LETTER')
36 tree=(index(controlcard,'MAKE_TREE').gt.0)
37 min_var=(index(controlcard,'MINVAR').gt.0)
38 plot_tree=(index(controlcard,'PLOT_TREE').gt.0)
39 punch_dist=(index(controlcard,'PUNCH_DIST').gt.0)
40 call readi(controlcard,'NCUT',ncut,0)
41 call readi(controlcard,'NCLUST',nclust,5)
42 call readi(controlcard,'NSTART',nstart,0)
43 call readi(controlcard,'NEND',nend,0)
44 call reada(controlcard,'ECUT',ecut,10.0d0)
45 call reada(controlcard,'PROB',prob_limit,0.99d0)
46 write (iout,*) "Probability limit",prob_limit
47 lgrp=(index(controlcard,'LGRP').gt.0)
48 caonly=(index(controlcard,'CA_ONLY').gt.0)
49 print_dist=(index(controlcard,'PRINT_DIST').gt.0)
51 & call multreada(controlcard,'CUTOFF',rcutoff,ncut,-1.0d0)
52 call readi(controlcard,'IOPT',iopt,2)
53 lside = index(controlcard,"SIDE").gt.0
54 efree = index(controlcard,"EFREE").gt.0
55 call readi(controlcard,'NTEMP',nT,1)
56 write (iout,*) "nT",nT
57 call multreada(controlcard,'TEMPER',beta_h,nT,300.0d0)
58 write (iout,*) "nT",nT
59 write (iout,*) 'beta_h',(beta_h(i),i=1,nT)
61 beta_h(i)=1.0d0/(1.987D-3*beta_h(i))
63 write (iout,*) 'beta_h',(beta_h(i),i=1,nT)
64 lprint_cart=index(controlcard,"PRINT_CART") .gt.0
65 lprint_int=index(controlcard,"PRINT_INT") .gt.0
66 with_dihed_constr = index(controlcard,"WITH_DIHED_CONSTR").gt.0
67 call readi(controlcard,'CONSTR_DIST',constr_dist,0)
68 write (iout,*) "with_dihed_constr ",with_dihed_constr,
69 & " CONSTR_DIST",constr_dist
71 call readi(controlcard,'CONSTR_HOMOL',constr_homology,0)
72 write (iout,*) "with_homology_constr ",with_dihed_constr,
73 & " CONSTR_HOMOLOGY",constr_homology
74 print_homology_restraints=
75 & index(controlcard,"PRINT_HOMOLOGY_RESTRAINTS").gt.0
76 print_contact_map=index(controlcard,"PRINT_CONTACT_MAP").gt.0
77 print_homology_models=
78 & index(controlcard,"PRINT_HOMOLOGY_MODELS").gt.0
88 c--------------------------------------------------------------------------
91 C Read molecular data.
95 include 'COMMON.IOUNITS'
98 include 'COMMON.INTERACT'
99 include 'COMMON.LOCAL'
100 include 'COMMON.NAMES'
101 include 'COMMON.CHAIN'
102 include 'COMMON.FFIELD'
103 include 'COMMON.SBRIDGE'
104 include 'COMMON.HEADER'
105 include 'COMMON.CONTROL'
106 include 'COMMON.CONTACTS'
107 include 'COMMON.TIME1'
108 include 'COMMON.TORCNSTR'
110 include 'COMMON.INFO'
112 character*4 sequence(maxres)
113 character*800 weightcard
115 double precision x(maxvar)
116 integer itype_pdb(maxres)
119 write (iout,*) " MOLREAD: NRES",NRES
123 C Read weights of the subsequent energy terms.
124 call card_concat(weightcard)
125 call reada(weightcard,'WSC',wsc,1.0d0)
126 call reada(weightcard,'WLONG',wsc,wsc)
127 call reada(weightcard,'WSCP',wscp,1.0d0)
128 call reada(weightcard,'WELEC',welec,1.0D0)
129 call reada(weightcard,'WVDWPP',wvdwpp,welec)
130 call reada(weightcard,'WEL_LOC',wel_loc,1.0D0)
131 call reada(weightcard,'WCORR4',wcorr4,0.0D0)
132 call reada(weightcard,'WCORR5',wcorr5,0.0D0)
133 call reada(weightcard,'WCORR6',wcorr6,0.0D0)
134 call reada(weightcard,'WTURN3',wturn3,1.0D0)
135 call reada(weightcard,'WTURN4',wturn4,1.0D0)
136 call reada(weightcard,'WTURN6',wturn6,1.0D0)
137 call reada(weightcard,'WSTRAIN',wstrain,1.0D0)
138 call reada(weightcard,'WBOND',wbond,1.0D0)
139 call reada(weightcard,'WTOR',wtor,1.0D0)
140 call reada(weightcard,'WTORD',wtor_d,1.0D0)
141 call reada(weightcard,'WANG',wang,1.0D0)
142 call reada(weightcard,'WSCLOC',wscloc,1.0D0)
143 call reada(weightcard,'SCAL14',scal14,0.4D0)
144 call reada(weightcard,'SCALSCP',scalscp,1.0d0)
145 call reada(weightcard,'CUTOFF',cutoff_corr,7.0d0)
146 call reada(weightcard,'DELT_CORR',delt_corr,0.5d0)
147 call reada(weightcard,'WSCCOR',wsccor,1.0D0)
148 call reada(weightcard,"D0CM",d0cm,3.78d0)
149 call reada(weightcard,"AKCM",akcm,15.1d0)
150 call reada(weightcard,"AKTH",akth,11.0d0)
151 call reada(weightcard,"AKCT",akct,12.0d0)
152 call reada(weightcard,"V1SS",v1ss,-1.08d0)
153 call reada(weightcard,"V2SS",v2ss,7.61d0)
154 call reada(weightcard,"V3SS",v3ss,13.7d0)
155 call reada(weightcard,"EBR",ebr,-5.50D0)
157 call reada(weightcard,'WDFAD',wdfa_dist,0.0d0)
158 call reada(weightcard,'WDFAT',wdfa_tor,0.0d0)
159 call reada(weightcard,'WDFAN',wdfa_nei,0.0d0)
160 call reada(weightcard,'WDFAB',wdfa_beta,0.0d0)
161 if (index(weightcard,'SOFT').gt.0) ipot=6
162 C 12/1/95 Added weight for the multi-body term WCORR
163 call reada(weightcard,'WCORRH',wcorr,1.0D0)
166 dyn_ssbond_ij(i,j)=1.0d300
169 call reada(weightcard,"HT",Ht,0.0D0)
171 ss_depth=ebr/wsc-0.25*eps(1,1)
172 Ht=Ht/wsc-0.25*eps(1,1)
173 akcm=akcm*wstrain/wsc
174 akth=akth*wstrain/wsc
175 akct=akct*wstrain/wsc
176 v1ss=v1ss*wstrain/wsc
177 v2ss=v2ss*wstrain/wsc
178 v3ss=v3ss*wstrain/wsc
180 ss_depth=ebr/wstrain-0.25*eps(1,1)*wsc/wstrain
182 write (iout,'(/a)') "Disulfide bridge parameters:"
183 write (iout,'(a,f10.2)') 'S-S bridge energy: ',ebr
184 write (iout,'(a,f10.2)') 'S-S depth: ',ss_depth
185 write (iout,'(2(a,f10.2))') 'd0cm:',d0cm,' akcm:',akcm
186 write (iout,'(2(a,f10.2))') 'akth:',akth,' akct:',akct
187 write (iout,'(3(a,f10.2))') 'v1ss:',v1ss,' v2ss:',v2ss,
189 write (iout,'(2(a,f10.2))') 'ht:',ht,' eps:', eps(1,1)
190 if (wcorr4.gt.0.0d0) wcorr=wcorr4
209 weights(22)=wdfa_dist
212 weights(25)=wdfa_beta
213 write (iout,10) wsc,wscp,welec,wvdwpp,wbond,wang,wscloc,wtor,
214 & wtor_d,wstrain,wel_loc,wcorr,wcorr5,wcorr6,wturn3,
215 & wturn4,wturn6,wsccor,wdfa_dist,wdfa_tor,wdfa_nei,wdfa_beta
216 10 format (/'Energy-term weights (unscaled):'//
217 & 'WSCC= ',f10.6,' (SC-SC)'/
218 & 'WSCP= ',f10.6,' (SC-p)'/
219 & 'WELEC= ',f10.6,' (p-p electr)'/
220 & 'WVDWPP= ',f10.6,' (p-p VDW)'/
221 & 'WBOND= ',f10.6,' (stretching)'/
222 & 'WANG= ',f10.6,' (bending)'/
223 & 'WSCLOC= ',f10.6,' (SC local)'/
224 & 'WTOR= ',f10.6,' (torsional)'/
225 & 'WTORD= ',f10.6,' (double torsional)'/
226 & 'WSTRAIN=',f10.6,' (SS bridges & dist. cnstr.)'/
227 & 'WEL_LOC=',f10.6,' (multi-body 3-rd order)'/
228 & 'WCORR4= ',f10.6,' (multi-body 4th order)'/
229 & 'WCORR5= ',f10.6,' (multi-body 5th order)'/
230 & 'WCORR6= ',f10.6,' (multi-body 6th order)'/
231 & 'WTURN3= ',f10.6,' (turns, 3rd order)'/
232 & 'WTURN4= ',f10.6,' (turns, 4th order)'/
233 & 'WTURN6= ',f10.6,' (turns, 6th order)'/
234 & 'WSCCOR= ',f10.6,' (SC-backbone torsional correalations)'/
235 & 'WDFAD= ',f10.6,' (DFA distance)'/
236 & 'WDFAT= ',f10.6,' (DFA torsional)'/
237 & 'WDFAN= ',f10.6,' (DFA neighbors)'/
238 & 'WDFAB= ',f10.6,' (DFA beta)'/)
239 if (wcorr4.gt.0.0d0) then
240 write (iout,'(/2a/)') 'Local-electrostatic type correlation ',
241 & 'between contact pairs of peptide groups'
242 write (iout,'(2(a,f5.3/))')
243 & 'Cutoff on 4-6th order correlation terms: ',cutoff_corr,
244 & 'Range of quenching the correlation terms:',2*delt_corr
245 else if (wcorr.gt.0.0d0) then
246 write (iout,'(/2a/)') 'Hydrogen-bonding correlation ',
247 & 'between contact pairs of peptide groups'
249 write (iout,'(a,f8.3)')
250 & 'Scaling factor of 1,4 SC-p interactions:',scal14
251 write (iout,'(a,f8.3)')
252 & 'General scaling factor of SC-p interactions:',scalscp
253 r0_corr=cutoff_corr-delt_corr
255 aad(i,1)=scalscp*aad(i,1)
256 aad(i,2)=scalscp*aad(i,2)
257 bad(i,1)=scalscp*bad(i,1)
258 bad(i,2)=scalscp*bad(i,2)
266 print *,'indpdb=',indpdb,' pdbref=',pdbref
268 C Read sequence if not taken from the pdb file.
269 if (iscode.gt.0) then
270 read (inp,'(80a1)') (sequence(i)(1:1),i=1,nres)
272 read (inp,'(20(1x,a3))') (sequence(i),i=1,nres)
274 C Convert sequence to numeric code
276 itype(i)=rescode(i,sequence(i),iscode)
278 if (itype(2).eq.10.and.itype(1).eq.ntyp1) then
280 & "Glycine is the first full residue, initial dummy deleted"
286 if (itype(nres-1).eq.10.and.itype(nres).eq.ntyp1) then
288 & "Glycine is the last full residue, terminal dummy deleted"
292 print '(20i4)',(itype(i),i=1,nres)
296 if (itype(i).eq.21 .or. itype(i+1).eq.21) then
298 if (itype(i).eq.21) then
302 else if (itype(i+1).ne.20) then
304 else if (itype(i).ne.20) then
311 write (iout,*) "ITEL"
313 write (iout,*) i,itype(i),itel(i)
316 print *,'Call Read_Bridge.'
318 if (with_dihed_constr) then
320 read (inp,*) ndih_constr
321 if (ndih_constr.gt.0) then
323 write (iout,*) 'FTORS',ftors
324 read (inp,*) (idih_constr(i),phi0(i),drange(i),i=1,ndih_constr)
326 & 'There are',ndih_constr,' constraints on phi angles.'
328 write (iout,'(i5,2f8.3)') idih_constr(i),phi0(i),drange(i)
331 phi0(i)=deg2rad*phi0(i)
332 drange(i)=deg2rad*drange(i)
340 print *,'NNT=',NNT,' NCT=',NCT
341 if (itype(1).eq.21) nnt=2
342 if (itype(nres).eq.21) nct=nct-1
343 if (nstart.lt.nnt) nstart=nnt
344 if (nend.gt.nct .or. nend.eq.0) nend=nct
345 write (iout,*) "nstart",nstart," nend",nend
348 C Juyong:READ init_vars
349 C Initialize variables!
350 C Juyong:READ read_info
351 C READ fragment information!!
352 C both routines should be in dfa.F file!!
354 if (.not. (wdfa_dist.eq.0.0 .and. wdfa_tor.eq.0.0 .and.
355 & wdfa_nei.eq.0.0 .and. wdfa_beta.eq.0.0)) then
357 write (iout,*) "Calling init_dfa_vars"
366 write (iout,*) 'init_dfa_vars finished!'
375 write (iout,*) 'read_dfa_info finished!'
384 if (constr_homology.gt.0) then
385 call read_constr_homology(print_homology_restraints)
389 c read(inp,'(a)') pdbfile
390 c write (iout,'(2a)') 'PDB data will be read from file ',pdbfile
391 c open(ipdbin,file=pdbfile,status='old',err=33)
393 c 33 write (iout,'(a)') 'Error opening PDB file.'
396 c print *,'Begin reading pdb data'
398 c print *,'Finished reading pdb data'
399 c write (iout,'(a,i3,a,i3)')'nsup=',nsup,' nstart_sup=',nstart_sup
401 c itype_pdb(i)=itype(i)
404 c write (iout,'(a,i3)') 'nsup=',nsup
406 c if (nsup.le.(nct-nnt+1)) then
407 c do i=0,nct-nnt+1-nsup
408 c if (seq_comp(itype(nnt+i),itype_pdb(nstart_sup),nsup)) then
414 c & 'Error - sequences to be superposed do not match.'
417 c do i=0,nsup-(nct-nnt+1)
418 c if (seq_comp(itype(nnt),itype_pdb(nstart_sup+i),nct-nnt+1))
420 c nstart_sup=nstart_sup+i
426 c & 'Error - sequences to be superposed do not match.'
429 c write (iout,*) 'nsup=',nsup,' nstart_sup=',nstart_sup,
430 c & ' nstart_seq=',nstart_seq
434 write (iout,*) "molread: REFSTR",refstr
436 if (.not.pdbref) then
437 call read_angles(inp,*38)
439 38 write (iout,'(a)') 'Error reading reference structure.'
441 call mp_stopall(Error_Msg)
443 stop 'Error reading reference structure'
455 call contact(print_contact_map,ncont_ref,icont_ref)
457 c Read distance restraints
458 if (constr_dist.gt.0) then
459 call read_dist_constr
464 c-----------------------------------------------------------------------------
465 logical function seq_comp(itypea,itypeb,length)
467 integer length,itypea(length),itypeb(length)
470 if (itypea(i).ne.itypeb(i)) then
478 c-----------------------------------------------------------------------------
479 subroutine read_bridge
480 C Read information about disulfide bridges.
483 include 'COMMON.IOUNITS'
486 include 'COMMON.INTERACT'
487 include 'COMMON.LOCAL'
488 include 'COMMON.NAMES'
489 include 'COMMON.CHAIN'
490 include 'COMMON.FFIELD'
491 include 'COMMON.SBRIDGE'
492 include 'COMMON.HEADER'
493 include 'COMMON.CONTROL'
494 include 'COMMON.TIME1'
496 include 'COMMON.INFO'
499 C Read bridging residues.
500 read (inp,*) ns,(iss(i),i=1,ns)
501 write(iout,*)'ns=',ns
502 C Check whether the specified bridging residues are cystines.
504 if (itype(iss(i)).ne.1) then
505 write (iout,'(2a,i3,a)')
506 & 'Do you REALLY think that the residue ',restyp(iss(i)),i,
507 & ' can form a disulfide bridge?!!!'
508 write (*,'(2a,i3,a)')
509 & 'Do you REALLY think that the residue ',restyp(iss(i)),i,
510 & ' can form a disulfide bridge?!!!'
512 call mp_stopall(error_msg)
518 C Read preformed bridges.
520 read (inp,*) nss,(ihpb(i),jhpb(i),i=1,nss)
523 C Check if the residues involved in bridges are in the specified list of
527 if (ihpb(i).eq.ihpb(j).or.ihpb(i).eq.jhpb(j)
528 & .or.jhpb(i).eq.ihpb(j).or.jhpb(i).eq.jhpb(j)) then
529 write (iout,'(a,i3,a)') 'Disulfide pair',i,
530 & ' contains residues present in other pairs.'
531 write (*,'(a,i3,a)') 'Disulfide pair',i,
532 & ' contains residues present in other pairs.'
534 call mp_stopall(error_msg)
541 if (ihpb(i).eq.iss(j)) goto 10
543 write (iout,'(a,i3,a)') 'Pair',i,' contains unknown cystine.'
546 if (jhpb(i).eq.iss(j)) goto 20
548 write (iout,'(a,i3,a)') 'Pair',i,' contains unknown cystine.'
559 if (ns.gt.0.and.dyn_ss) then
563 forcon(i-nss)=forcon(i)
570 dyn_ss_mask(iss(i))=.true.
571 c write(iout,*) i,iss(i),dyn_ss_mask(iss(i)),"ATU"
574 print *, "Leaving brigde read"
577 c----------------------------------------------------------------------------
578 subroutine read_angles(kanal,*)
583 include 'COMMON.CHAIN'
584 include 'COMMON.IOUNITS'
586 read (kanal,*,err=10,end=10) (theta(i),i=3,nres)
587 read (kanal,*,err=10,end=10) (phi(i),i=4,nres)
588 read (kanal,*,err=10,end=10) (alph(i),i=2,nres-1)
589 read (kanal,*,err=10,end=10) (omeg(i),i=2,nres-1)
591 theta(i)=deg2rad*theta(i)
592 phi(i)=deg2rad*phi(i)
593 alph(i)=deg2rad*alph(i)
594 omeg(i)=deg2rad*omeg(i)
599 c----------------------------------------------------------------------------
600 subroutine reada(rekord,lancuch,wartosc,default)
602 character*(*) rekord,lancuch
603 double precision wartosc,default
606 iread=index(rekord,lancuch)
611 iread=iread+ilen(lancuch)+1
612 read (rekord(iread:),*) wartosc
615 c----------------------------------------------------------------------------
616 subroutine multreada(rekord,lancuch,tablica,dim,default)
619 double precision tablica(dim),default
620 character*(*) rekord,lancuch
626 iread=index(rekord,lancuch)
627 if (iread.eq.0) return
628 iread=iread+ilen(lancuch)+1
629 read (rekord(iread:),*,end=10,err=10) (tablica(i),i=1,dim)
632 c----------------------------------------------------------------------------
633 subroutine readi(rekord,lancuch,wartosc,default)
635 character*(*) rekord,lancuch
636 integer wartosc,default
639 iread=index(rekord,lancuch)
644 iread=iread+ilen(lancuch)+1
645 read (rekord(iread:),*) wartosc
648 c----------------------------------------------------------------------------
649 subroutine multreadi(rekord,lancuch,tablica,dim,default)
652 integer tablica(dim),default
653 character*(*) rekord,lancuch
660 iread=index(rekord,lancuch(:ilen(lancuch))//"=")
661 if (iread.eq.0) return
662 iread=iread+ilen(lancuch)+1
663 read (rekord(iread:),*,end=10,err=10) (tablica(i),i=1,dim)
666 c----------------------------------------------------------------------------
667 subroutine card_concat(card)
669 include 'COMMON.IOUNITS'
671 character*80 karta,ucase
673 read (inp,'(a)') karta
676 do while (karta(80:80).eq.'&')
677 card=card(:ilen(card)+1)//karta(:79)
678 read (inp,'(a)') karta
681 card=card(:ilen(card)+1)//karta
684 c----------------------------------------------------------------------------
693 include 'COMMON.IOUNITS'
694 include 'COMMON.CONTROL'
695 integer lenpre,lenpot,ilen
697 character*16 cformat,cprint
699 integer lenint,lenout
700 call getenv('INPUT',prefix)
701 call getenv('OUTPUT',prefout)
702 call getenv('INTIN',prefintin)
703 call getenv('COORD',cformat)
704 call getenv('PRINTCOOR',cprint)
705 call getenv('SCRATCHDIR',scratchdir)
708 if (index(ucase(cformat),'CX').gt.0) then
715 lenint=ilen(prefintin)
716 C Get the names and open the input files
717 open (inp,file=prefix(:ilen(prefix))//'.inp',status='old')
719 write (liczba,'(bz,i3.3)') me
720 outname=prefout(:lenout)//'_clust.out_'//liczba
722 outname=prefout(:lenout)//'_clust.out'
725 intinname=prefintin(:lenint)//'.bx'
726 else if (from_cx) then
727 intinname=prefintin(:lenint)//'.cx'
729 intinname=prefintin(:lenint)//'.int'
731 rmsname=prefintin(:lenint)//'.rms'
732 open (jplot,file=prefout(:ilen(prefout))//'.tex',
734 open (jrms,file=rmsname,status='unknown')
735 open(iout,file=outname,status='unknown')
736 C Get parameter filenames and open the parameter files.
737 call getenv('BONDPAR',bondname)
738 open (ibond,file=bondname,status='old')
739 call getenv('THETPAR',thetname)
740 open (ithep,file=thetname,status='old')
741 call getenv('ROTPAR',rotname)
742 open (irotam,file=rotname,status='old')
743 call getenv('TORPAR',torname)
744 open (itorp,file=torname,status='old')
745 call getenv('TORDPAR',tordname)
746 open (itordp,file=tordname,status='old')
747 call getenv('FOURIER',fouriername)
748 open (ifourier,file=fouriername,status='old')
749 call getenv('ELEPAR',elename)
750 open (ielep,file=elename,status='old')
751 call getenv('SIDEPAR',sidename)
752 open (isidep,file=sidename,status='old')
753 call getenv('SIDEP',sidepname)
754 open (isidep1,file=sidepname,status="old")
755 call getenv('SCCORPAR',sccorname)
756 open (isccor,file=sccorname,status="old")
759 C 8/9/01 In the newest version SCp interaction constants are read from a file
760 C Use -DOLDSCP to use hard-coded constants instead.
762 call getenv('SCPPAR',scpname)
763 open (iscpp,file=scpname,status='old')
767 c-------------------------------------------------------------------------------
768 subroutine read_dist_constr
769 implicit real*8 (a-h,o-z)
771 include 'COMMON.CONTROL'
772 include 'COMMON.CHAIN'
773 include 'COMMON.IOUNITS'
774 include 'COMMON.SBRIDGE'
775 integer ifrag_(2,100),ipair_(2,100)
776 double precision wfrag_(100),wpair_(100)
777 character*500 controlcard
778 c write (iout,*) "Calling read_dist_constr"
779 c write (iout,*) "nres",nres," nstart_sup",nstart_sup," nsup",nsup
780 call card_concat(controlcard)
782 c write (iout,'(a)') controlcard
783 call readi(controlcard,"NFRAG",nfrag_,0)
784 call readi(controlcard,"NPAIR",npair_,0)
785 call readi(controlcard,"NDIST",ndist_,0)
786 call reada(controlcard,'DIST_CUT',dist_cut,5.0d0)
787 call multreadi(controlcard,"IFRAG",ifrag_(1,1),2*nfrag_,0)
788 call multreadi(controlcard,"IPAIR",ipair_(1,1),2*npair_,0)
789 call multreada(controlcard,"WFRAG",wfrag_(1),nfrag_,0.0d0)
790 call multreada(controlcard,"WPAIR",wpair_(1),npair_,0.0d0)
791 write (iout,*) "NFRAG",nfrag_," NPAIR",npair_," NDIST",ndist_
792 write (iout,*) "IFRAG"
794 write (iout,*) i,ifrag_(1,i),ifrag_(2,i),wfrag_(i)
796 write (iout,*) "IPAIR"
798 write (iout,*) i,ipair_(1,i),ipair_(2,i),wpair_(i)
805 if (.not.refstr .and. nfrag_.gt.0) then
807 & "ERROR: no reference structure to compute distance restraints"
809 & "Restraints must be specified explicitly (NDIST=number)"
812 if (nfrag_.lt.2 .and. npair_.gt.0) then
813 write (iout,*) "ERROR: Less than 2 fragments specified",
814 & " but distance restraints between pairs requested"
823 if (ifrag_(1,i).lt.nstart_sup) ifrag_(1,i)=nstart_sup
824 if (ifrag_(2,i).gt.nstart_sup+nsup-1)
825 & ifrag_(2,i)=nstart_sup+nsup-1
826 c write (iout,*) i,ifrag_(1,i),ifrag_(2,i),wfrag_(i)
828 if (wfrag_(i).gt.0.0d0) then
829 do j=ifrag_(1,i),ifrag_(2,i)-1
831 write (iout,*) "j",j," k",k
833 if (constr_dist.eq.1) then
838 forcon(nhpb)=wfrag_(i)
839 else if (constr_dist.eq.2) then
840 if (ddjk.le.dist_cut) then
845 forcon(nhpb)=wfrag_(i)
852 forcon(nhpb)=wfrag_(i)*dexp(-0.5d0*(ddjk/dist_cut)**2)
854 write (iout,'(a,3i5,f8.2,1pe12.2)') "+dist.constr ",
855 & nhpb,ihpb(nhpb),jhpb(nhpb),dhpb(nhpb),forcon(nhpb)
861 if (wpair_(i).gt.0.0d0) then
869 do j=ifrag_(1,ii),ifrag_(2,ii)
870 do k=ifrag_(1,jj),ifrag_(2,jj)
874 forcon(nhpb)=wpair_(i)
876 write (iout,'(a,3i5,f8.2,f10.1)') "+dist.constr ",
877 & nhpb,ihpb(nhpb),jhpb(nhpb),dhpb(nhpb),forcon(nhpb)
883 read (inp,*) ihpb(nhpb+1),jhpb(nhpb+1),dhpb(i),dhpb1(i),
884 & ibecarb(i),forcon(nhpb+1)
885 if (forcon(nhpb+1).gt.0.0d0) then
887 if (ibecarb(i).gt.0) then
891 if (dhpb(nhpb).eq.0.0d0)
892 & dhpb(nhpb)=dist(ihpb(nhpb),jhpb(nhpb))
896 write (iout,'(a,3i5,2f8.2,i2,f10.1)') "+dist.constr ",
897 & i,ihpb(i),jhpb(i),dhpb(i),dhpb1(i),ibecarb(i),forcon(i)
907 c====-------------------------------------------------------------------
908 subroutine read_constr_homology(lprn)
914 include 'COMMON.SETUP'
915 include 'COMMON.CONTROL'
916 include 'COMMON.CHAIN'
917 include 'COMMON.IOUNITS'
919 include 'COMMON.INTERACT'
920 include 'COMMON.HOMRESTR'
925 c include 'include_unres/COMMON.VAR'
928 c double precision odl_temp,sigma_odl_temp,waga_theta,waga_d,
930 c common /przechowalnia/ odl_temp(maxres,maxres,max_template),
931 c & sigma_odl_temp(maxres,maxres,max_template)
933 character*24 model_ki_dist, model_ki_angle
934 character*500 controlcard
935 integer ki, i, j, k, l, ii_in_use(maxdim),i_tmp,idomain_tmp
936 integer idomain(max_template,maxres)
942 c FP - Nov. 2014 Temporary specifications for new vars
944 double precision rescore_tmp,x12,y12,z12,rescore2_tmp
945 double precision, dimension (max_template,maxres) :: rescore
946 double precision, dimension (max_template,maxres) :: rescore2
947 character*24 tpl_k_rescore
948 c -----------------------------------------------------------------
949 c Reading multiple PDB ref structures and calculation of retraints
950 c not using pre-computed ones stored in files model_ki_{dist,angle}
952 c -----------------------------------------------------------------
955 c Alternative: reading from input
957 write (iout,*) "BEGIN READ HOMOLOGY INFO"
964 call card_concat(controlcard)
965 call reada(controlcard,"HOMOL_DIST",waga_dist,1.0d0)
966 call reada(controlcard,"HOMOL_ANGLE",waga_angle,1.0d0)
967 call reada(controlcard,"HOMOL_THETA",waga_theta,1.0d0) ! new
968 call reada(controlcard,"HOMOL_SCD",waga_d,1.0d0) ! new
969 call reada(controlcard,'DIST_CUT',dist_cut,5.0d0) ! for diff ways of calc sigma
970 call reada(controlcard,'DIST2_CUT',dist2_cut,9999.0d0)
971 call readi(controlcard,"HOMOL_NSET",homol_nset,1)
972 read2sigma=(index(controlcard,'READ2SIGMA').gt.0)
973 if (homol_nset.gt.1)then
974 call readi(controlcard,"ISET",iset,1)
975 call card_concat(controlcard)
976 read(controlcard,*) (waga_homology(i),i=1,homol_nset)
983 write(iout,*) "read_constr_homology iset",iset
984 write(iout,*) "waga_homology(",iset,")",waga_homology(iset)
991 cd write (iout,*) "nnt",nnt," nct",nct
1003 c Reading HM global scores (prob not required)
1006 do k=1,constr_homology
1010 c open (4,file="HMscore")
1011 c do k=1,constr_homology
1012 c read (4,*,end=521) hmscore_tmp
1013 c hmscore(k)=hmscore_tmp ! Another transformation can be used
1014 c write(*,*) "Model", k, ":", hmscore(k)
1025 c write(iout,*) "waga_theta",waga_theta,"waga_d",waga_d
1027 write (iout,*) "CONSTR_HOMOLOGY",constr_homology
1028 do k=1,constr_homology
1030 read(inp,'(a)') pdbfile
1031 c write (iout,*) "k ",k," pdbfile ",pdbfile
1032 c Next stament causes error upon compilation (?)
1033 c if(me.eq.king.or. .not. out1file)
1034 c write (iout,'(2a)') 'PDB data will be read from file ',
1035 c & pdbfile(:ilen(pdbfile))
1036 write (iout,'(a,5x,a)') 'HOMOL: Opening PDB file',
1037 & pdbfile(:ilen(pdbfile))
1038 open(ipdbin,file=pdbfile,status='old',err=33)
1040 33 write (iout,'(a,5x,a)') 'Error opening PDB file',
1041 & pdbfile(:ilen(pdbfile))
1044 c print *,'Begin reading pdb data'
1046 c Files containing res sim or local scores (former containing sigmas)
1049 write(kic2,'(bz,i2.2)') k
1051 tpl_k_rescore="template"//kic2//".sco"
1057 crefjlee(j,i)=c(j,i)
1062 write (iout,'(i5,3f8.3,5x,3f8.3)') i,(crefjlee(j,i),j=1,3),
1063 & (crefjlee(j,i+nres),j=1,3)
1065 write (iout,*) "READ HOMOLOGY INFO"
1066 write (iout,*) "read_constr_homology x: after reading pdb file"
1067 write (iout,*) "waga_homology(",iset,")",waga_homology(iset)
1068 write (iout,*) "waga_dist",waga_dist
1069 write (iout,*) "waga_angle",waga_angle
1070 write (iout,*) "waga_theta",waga_theta
1071 write (iout,*) "waga_d",waga_d
1072 write (iout,*) "dist_cut",dist_cut
1081 c Distance restraints
1084 C Copy the coordinates from reference coordinates (?)
1088 c write (iout,*) "c(",j,i,") =",c(j,i)
1092 c From read_dist_constr (commented out 25/11/2014 <-> res sim)
1094 c write(iout,*) "tpl_k_rescore - ",tpl_k_rescore
1095 open (ientin,file=tpl_k_rescore,status='old')
1096 if (nnt.gt.1) rescore(k,1)=0.0d0
1097 do irec=nnt,maxdim ! loop for reading res sim
1098 if (read2sigma) then
1099 read (ientin,*,end=1401) i_tmp,rescore2_tmp,rescore_tmp,
1102 idomain(k,i_tmp)=idomain_tmp
1103 rescore(k,i_tmp)=rescore_tmp
1104 rescore2(k,i_tmp)=rescore2_tmp
1107 read (ientin,*,end=1401) rescore_tmp
1109 c rescore(k,irec)=rescore_tmp+1.0d0 ! to avoid 0 values
1110 rescore(k,irec)=0.5d0*(rescore_tmp+0.5d0) ! alt transf to reduce scores
1111 c write(iout,*) "rescore(",k,irec,") =",rescore(k,irec)
1116 if (waga_dist.ne.0.0d0) then
1124 distal=dsqrt(x12*x12+y12*y12+z12*z12)
1125 c write (iout,*) k,i,j,distal,dist2_cut
1127 if (idomain(k,i).eq.idomain(k,j).and.idomain(k,i).ne.0
1128 & .and. distal.le.dist2_cut ) then
1134 c write (iout,*) "k",k
1135 c write (iout,*) "i",i," j",j," constr_homology",
1140 if (read2sigma) then
1143 sigma_odl(k,ii)=sigma_odl(k,ii)+rescore2(k,ik)
1145 sigma_odl(k,ii)=sigma_odl(k,ii)/(j-i+1)
1146 if (odl(k,ii).gt.dist_cut) sigma_odl(k,ii) =
1147 & sigma_odl(k,ii)*dexp(0.5d0*(odl(k,ii)/dist_cut)**2-0.5d0)
1149 if (odl(k,ii).le.dist_cut) then
1150 sigma_odl(k,ii)=rescore(k,i)+rescore(k,j)
1153 sigma_odl(k,ii)=(rescore(k,i)+rescore(k,j))*
1154 & dexp(0.5d0*(odl(k,ii)/dist_cut)**2)
1156 sigma_odl(k,ii)=(rescore(k,i)+rescore(k,j))*
1157 & dexp(0.5d0*(odl(k,ii)/dist_cut)**2-0.5d0)
1161 sigma_odl(k,ii)=1.0d0/(sigma_odl(k,ii)*sigma_odl(k,ii))
1164 l_homo(k,ii)=.false.
1171 c Theta, dihedral and SC retraints
1173 if (waga_angle.gt.0.0d0) then
1174 c open (ientin,file=tpl_k_sigma_dih,status='old')
1175 c do irec=1,maxres-3 ! loop for reading sigma_dih
1176 c read (ientin,*,end=1402) i,j,ki,l,sigma_dih(k,i+nnt-1) ! j,ki,l what for?
1177 c if (i+nnt-1.gt.lim_dih) lim_dih=i+nnt-1 ! right?
1178 c sigma_dih(k,i+nnt-1)=sigma_dih(k,i+nnt-1)* ! not inverse because of use of res. similarity
1179 c & sigma_dih(k,i+nnt-1)
1184 if (idomain(k,i).eq.0) then
1188 dih(k,i)=phiref(i) ! right?
1189 c read (ientin,*) sigma_dih(k,i) ! original variant
1190 c write (iout,*) "dih(",k,i,") =",dih(k,i)
1191 c write(iout,*) "rescore(",k,i,") =",rescore(k,i),
1192 c & "rescore(",k,i-1,") =",rescore(k,i-1),
1193 c & "rescore(",k,i-2,") =",rescore(k,i-2),
1194 c & "rescore(",k,i-3,") =",rescore(k,i-3)
1196 sigma_dih(k,i)=(rescore(k,i)+rescore(k,i-1)+
1197 & rescore(k,i-2)+rescore(k,i-3))/4.0
1198 c if (read2sigma) sigma_dih(k,i)=sigma_dih(k,i)/4.0
1199 c write (iout,*) "Raw sigmas for dihedral angle restraints"
1200 c write (iout,'(i5,10(2f8.2,4x))') i,sigma_dih(k,i)
1201 c sigma_dih(k,i)=hmscore(k)*rescore(k,i)*rescore(k,i-1)*
1202 c rescore(k,i-2)*rescore(k,i-3) ! right expression ?
1203 c Instead of res sim other local measure of b/b str reliability possible
1204 sigma_dih(k,i)=1.0d0/(sigma_dih(k,i)*sigma_dih(k,i))
1205 c sigma_dih(k,i)=sigma_dih(k,i)*sigma_dih(k,i)
1210 if (waga_theta.gt.0.0d0) then
1211 c open (ientin,file=tpl_k_sigma_theta,status='old')
1212 c do irec=1,maxres-2 ! loop for reading sigma_theta, right bounds?
1213 c read (ientin,*,end=1403) i,j,ki,sigma_theta(k,i+nnt-1) ! j,ki what for?
1214 c sigma_theta(k,i+nnt-1)=sigma_theta(k,i+nnt-1)* ! not inverse because of use of res. similarity
1215 c & sigma_theta(k,i+nnt-1)
1220 do i = nnt+2,nct ! right? without parallel.
1221 c do i = i=1,nres ! alternative for bounds acc to readpdb?
1222 c do i=ithet_start,ithet_end ! with FG parallel.
1223 if (idomain(k,i).eq.0) then
1224 sigma_theta(k,i)=0.0
1227 thetatpl(k,i)=thetaref(i)
1228 c write (iout,*) "thetatpl(",k,i,") =",thetatpl(k,i)
1229 c write(iout,*) "rescore(",k,i,") =",rescore(k,i),
1230 c & "rescore(",k,i-1,") =",rescore(k,i-1),
1231 c & "rescore(",k,i-2,") =",rescore(k,i-2)
1232 c read (ientin,*) sigma_theta(k,i) ! 1st variant
1233 sigma_theta(k,i)=(rescore(k,i)+rescore(k,i-1)+
1234 & rescore(k,i-2))/3.0
1235 c if (read2sigma) sigma_theta(k,i)=sigma_theta(k,i)/3.0
1236 sigma_theta(k,i)=1.0d0/(sigma_theta(k,i)*sigma_theta(k,i))
1238 c sigma_theta(k,i)=hmscore(k)*rescore(k,i)*rescore(k,i-1)*
1239 c rescore(k,i-2) ! right expression ?
1240 c sigma_theta(k,i)=sigma_theta(k,i)*sigma_theta(k,i)
1245 if (waga_d.gt.0.0d0) then
1246 c open (ientin,file=tpl_k_sigma_d,status='old')
1247 c do irec=1,maxres-1 ! loop for reading sigma_theta, right bounds?
1248 c read (ientin,*,end=1404) i,j,sigma_d(k,i+nnt-1) ! j,ki what for?
1249 c sigma_d(k,i+nnt-1)=sigma_d(k,i+nnt-1)* ! not inverse because of use of res. similarity
1250 c & sigma_d(k,i+nnt-1)
1254 do i = nnt,nct ! right? without parallel.
1255 c do i=2,nres-1 ! alternative for bounds acc to readpdb?
1256 c do i=loc_start,loc_end ! with FG parallel.
1257 if (itype(i).eq.10) cycle
1258 if (idomain(k,i).eq.0 ) then
1265 c write (iout,*) "xxtpl(",k,i,") =",xxtpl(k,i)
1266 c write (iout,*) "yytpl(",k,i,") =",yytpl(k,i)
1267 c write (iout,*) "zztpl(",k,i,") =",zztpl(k,i)
1268 c write(iout,*) "rescore(",k,i,") =",rescore(k,i)
1269 sigma_d(k,i)=rescore(k,i) ! right expression ?
1270 sigma_d(k,i)=1.0d0/(sigma_d(k,i)*sigma_d(k,i))
1272 c sigma_d(k,i)=hmscore(k)*rescore(k,i) ! right expression ?
1273 c sigma_d(k,i)=sigma_d(k,i)*sigma_d(k,i)
1274 c read (ientin,*) sigma_d(k,i) ! 1st variant
1275 if (i-nnt+1.gt.lim_xx) lim_xx=i-nnt+1 ! right?
1281 c remove distance restraints not used in any model from the list
1282 c shift data in all arrays
1284 if (waga_dist.ne.0.0d0) then
1289 if (ii_in_use(ii).eq.0) then
1291 ires_homo(ki)=ires_homo(ki+1)
1292 jres_homo(ki)=jres_homo(ki+1)
1293 ii_in_use(ki)=ii_in_use(ki+1)
1294 do k=1,constr_homology
1295 odl(k,ki)=odl(k,ki+1)
1296 sigma_odl(k,ki)=sigma_odl(k,ki+1)
1297 l_homo(k,ki)=l_homo(k,ki+1)
1306 if (constr_homology.gt.0) call homology_partition
1307 if (constr_homology.gt.0) call init_int_table
1308 cd write (iout,*) "homology_partition: lim_theta= ",lim_theta,
1309 cd & "lim_xx=",lim_xx
1310 c write (iout,*) "ithet_start =",ithet_start,"ithet_end =",ithet_end
1311 c write (iout,*) "loc_start =",loc_start,"loc_end =",loc_end
1315 if (.not.lprn) return
1316 cd write(iout,*) "waga_theta",waga_theta,"waga_d",waga_d
1317 if(me.eq.king .or. .not. out1file .and. fg_rank.eq.0) then
1318 write (iout,*) "Distance restraints from templates"
1320 write(iout,'(3i5,100(2f8.2,1x,l1,4x))')
1321 & ii,ires_homo(ii),jres_homo(ii),
1322 & (odl(ki,ii),1.0d0/dsqrt(sigma_odl(ki,ii)),l_homo(ki,ii),
1323 & ki=1,constr_homology)
1325 write (iout,*) "Dihedral angle restraints from templates"
1327 write (iout,'(i5,100(2f8.2,4x))') i,(rad2deg*dih(ki,i),
1328 & rad2deg/dsqrt(sigma_dih(ki,i)),ki=1,constr_homology)
1330 write (iout,*) "Virtual-bond angle restraints from templates"
1331 do i=nnt+2,lim_theta
1332 write (iout,'(i5,100(2f8.2,4x))') i,(rad2deg*thetatpl(ki,i),
1333 & rad2deg/dsqrt(sigma_theta(ki,i)),ki=1,constr_homology)
1335 write (iout,*) "SC restraints from templates"
1337 write(iout,'(i5,100(4f8.2,4x))') i,
1338 & (xxtpl(ki,i),yytpl(ki,i),zztpl(ki,i),
1339 & 1.0d0/dsqrt(sigma_d(ki,i)),ki=1,constr_homology)
1342 c -----------------------------------------------------------------
1345 c----------------------------------------------------------------------