X-Git-Url: http://mmka.chem.univ.gda.pl/gitweb/?a=blobdiff_plain;f=source%2Funres%2Fsrc-HCD-5D%2Freadrtns_CSA.F;h=f120ec73dda73e1b91b77eeec9c619204391fb46;hb=3d04f1babd4ae90f9a0b8f256a2ce0a2c5751f33;hp=4765a4145257749827351bc3cb42ef016e6fbcac;hpb=5836ecdab5a8b95f079bbf6e07374dee3fce8a26;p=unres.git diff --git a/source/unres/src-HCD-5D/readrtns_CSA.F b/source/unres/src-HCD-5D/readrtns_CSA.F index 4765a41..f120ec7 100644 --- a/source/unres/src-HCD-5D/readrtns_CSA.F +++ b/source/unres/src-HCD-5D/readrtns_CSA.F @@ -171,13 +171,14 @@ c call readi(controlcard,'IZ_SC',iz_sc,0) timlim=60.0D0*timlim safety = 60.0d0*safety modecalc=0 + call readi(controlcard,"INTER_LIST_UPDATE",imatupdate,100) call reada(controlcard,"T_BATH",t_bath,300.0d0) minim=(index(controlcard,'MINIMIZE').gt.0) dccart=(index(controlcard,'CART').gt.0) overlapsc=(index(controlcard,'OVERLAP').gt.0) overlapsc=.not.overlapsc - searchsc=(index(controlcard,'NOSEARCHSC').gt.0) - searchsc=.not.searchsc + searchsc=(index(controlcard,'SEARCHSC').gt.0 .and. + & index(controlcard,'NOSEARCHSC').eq.0) sideadd=(index(controlcard,'SIDEADD').gt.0) energy_dec=(index(controlcard,'ENERGY_DEC').gt.0) mremd_dec=(index(controlcard,'MREMD_DEC').gt.0) @@ -186,7 +187,6 @@ c call readi(controlcard,'IZ_SC',iz_sc,0) pdbref=(index(controlcard,'PDBREF').gt.0) refstr=pdbref .or. (index(controlcard,'REFSTR').gt.0) indpdb=index(controlcard,'PDBSTART') - extconf=(index(controlcard,'EXTCONF').gt.0) AFMlog=(index(controlcard,'AFM')) selfguide=(index(controlcard,'SELFGUIDE')) c print *,'AFMlog',AFMlog,selfguide,"KUPA" @@ -295,6 +295,12 @@ cfmc modecalc=10 indphi=index(controlcard,'PHI') indback=index(controlcard,'BACK') iranconf=index(controlcard,'RAND_CONF') + start_from_model=(index(controlcard,'START_FROM_MODELS').gt.0) + extconf=(index(controlcard,'EXTCONF').gt.0) + if (start_from_model) then + iranconf=0 + extconf=.false. + endif i2ndstr=index(controlcard,'USE_SEC_PRED') gradout=index(controlcard,'GRADOUT').gt.0 gnorm_check=index(controlcard,'GNORM_CHECK').gt.0 @@ -546,6 +552,10 @@ c if performing umbrella sampling, fragments constrained are read from the frag & "Initial time step of numerical integration:",d_time, & " natural units" write (iout,'(60x,f10.5,a)') d_time*48.9," fs" + write (iout,'(a60,f10.5,a)') "Cutoff on interactions",r_cut_int, + & " A" + write(iout,'(a60,i5)')"Frequency of updating interaction list", + & imatupdate if (RESPA) then write (iout,'(2a,i4,a)') & "A-MTS algorithm used; initial time step for fast-varying", @@ -731,7 +741,7 @@ C integer ilen external ilen integer iperm,tperm - integer i,j,ii,k,l,itrial,itmp,i1,i2,it1,it2 + integer i,j,ii,k,l,itrial,itmp,i1,i2,it1,it2,nres_temp double precision sumv C C Read PDB structure if applicable @@ -826,7 +836,7 @@ c print '(20i4)',(itype(i),i=1,nres) do i=1,nres-1 write (iout,*) i,itype(i),itel(i) enddo - print *,'Call Read_Bridge.' +c print *,'Call Read_Bridge.' endif nnt=1 nct=nres @@ -839,7 +849,7 @@ cd print *,'NNT=',NNT,' NCT=',NCT chain_border1(1,i)=chain_border(1,i)-1 chain_border1(2,i)=chain_border(2,i)+1 enddo - chain_border1(1,nchain)=chain_border(1,nchain)-1 + if (nchain.gt.1) chain_border1(1,nchain)=chain_border(1,nchain)-1 chain_border1(2,nchain)=nres write(iout,*) "nres",nres," nchain",nchain do i=1,nchain @@ -865,9 +875,9 @@ c enddo if (.not. (wdfa_dist.eq.0.0 .and. wdfa_tor.eq.0.0 .and. & wdfa_nei.eq.0.0 .and. wdfa_beta.eq.0.0)) then call init_dfa_vars - print*, 'init_dfa_vars finished!' +c print*, 'init_dfa_vars finished!' call read_dfa_info - print*, 'read_dfa_info finished!' +c print*, 'read_dfa_info finished!' endif #endif if (pdbref) then @@ -1092,10 +1102,10 @@ czscore call geom_to_var(nvar,coord_exp_zs(1,1)) endif endif c print *, "A TU" - write (iout,*) "constr_dist",constr_dist,nstart_sup,nsup +c write (iout,*) "constr_dist",constr_dist,nstart_sup,nsup call flush(iout) if (constr_dist.gt.0) call read_dist_constr - write (iout,*) "After read_dist_constr nhpb",nhpb +c write (iout,*) "After read_dist_constr nhpb",nhpb if ((AFMlog.gt.0).or.(selfguide.gt.0)) call read_afminp call hpb_partition call NMRpeak_partition @@ -1158,23 +1168,69 @@ c print *, "A TU" enddo else homol_nset=0 + if (start_from_model) then + nmodel_start=0 + do + read(inp,'(a)',end=332,err=332) pdbfile + if (me.eq.king .or. .not. out1file) + & write (iout,'(a,5x,a)') 'Opening PDB file', + & pdbfile(:ilen(pdbfile)) + open(ipdbin,file=pdbfile,status='old',err=336) + goto 335 + 336 write (iout,'(a,5x,a)') 'Error opening PDB file', + & pdbfile(:ilen(pdbfile)) + call flush(iout) + stop + 335 continue + unres_pdb=.false. + nres_temp=nres + call readpdb + close(ipdbin) + if (nres.ge.nres_temp) then + nmodel_start=nmodel_start+1 + pdbfiles_chomo(nmodel_start)=pdbfile + do i=1,2*nres + do j=1,3 + chomo(j,i,nmodel_start)=c(j,i) + enddo + enddo + else + if (me.eq.king .or. .not. out1file) + & write (iout,'(a,2i5,1x,a)') + & "Different number of residues",nres_temp,nres, + & " model skipped." + endif + nres=nres_temp + enddo + 332 continue + if (nmodel_start.eq.0) then + if (me.eq.king .or. .not. out1file) + & write (iout,'(a)') + & "No valid starting model found START_FROM_MODELS is OFF" + start_from_model=.false. + endif + write (iout,*) "nmodel_start",nmodel_start + endif endif C endif +c write (iout,*) "iranconf",iranconf," extconf",extconf, +c & " start_from_models",start_from_model if (indpdb.eq.0 .and. modecalc.ne.2 .and. modecalc.ne.4 & .and. modecalc.ne.8 .and. modecalc.ne.9 .and. & modecalc.ne.10) then C If input structure hasn't been supplied from the PDB file read or generate C initial geometry. - if (iranconf.eq.0 .and. .not. extconf) then + if (iranconf.eq.0 .and. .not. extconf .and. .not. + & start_from_model) then if(me.eq.king.or..not.out1file .and.fg_rank.eq.0) & write (iout,'(a)') 'Initial geometry will be read in.' if (read_cart) then read(inp,'(8f10.5)',end=36,err=36) & ((c(l,k),l=1,3),k=1,nres), & ((c(l,k+nres),l=1,3),k=nnt,nct) - write (iout,*) "Exit READ_CART" +c write (iout,*) "Exit READ_CART" c write (iout,'(8f10.5)') c & ((c(l,k),l=1,3),k=1,nres), c & ((c(l,k+nres),l=1,3),k=nnt,nct) @@ -1400,7 +1456,13 @@ C Read information about disulfide bridges. integer i,j C Read bridging residues. read (inp,*) ns,(iss(i),i=1,ns) - print *,'ns=',ns +c 5/24/2020 Adam: Added a table to translate residue numbers to cysteine +c numbers + icys=0 + do i=1,ns + icys(iss(i))=i + enddo +c print *,'ns=',ns if(me.eq.king.or..not.out1file) & write (iout,*) 'ns=',ns,' iss:',(iss(i),i=1,ns) C Check whether the specified bridging residues are cystines. @@ -1609,9 +1671,11 @@ C Generate CA distance constraints. include 'COMMON.CONTROL' include 'COMMON.DBASE' include 'COMMON.THREAD' + include 'COMMON.SPLITELE' include 'COMMON.TIME1' integer i,j,itype_pdb(maxres) common /pizda/ itype_pdb + double precision dd double precision dist character*2 iden cd print *,'gen_dist_constr: nnt=',nnt,' nct=',nct @@ -1622,11 +1686,14 @@ cd & ' nsup',nsup cd write (2,*) 'i',i,' seq ',restyp(itype(i+nstart_seq-nstart_sup)), cd & ' seq_pdb', restyp(itype_pdb(i)) do j=i+2,nstart_sup+nsup-1 +c 5/24/2020 Adam: Cutoff included to reduce array size + dd = dist(i,j) + if (dd.gt.r_cut_int) cycle nhpb=nhpb+1 ihpb(nhpb)=i+nstart_seq-nstart_sup jhpb(nhpb)=j+nstart_seq-nstart_sup forcon(nhpb)=weidis - dhpb(nhpb)=dist(i,j) + dhpb(nhpb)=dd enddo enddo cd write (iout,'(a)') 'Distance constraints:' @@ -2370,10 +2437,10 @@ c------------------------------------------------------------------------------ open(irest2,file=rest2name,status='unknown') read(irest2,*) totT,EK,potE,totE,t_bath totTafm=totT - do i=1,2*nres + do i=0,2*nres-1 read(irest2,'(3e15.5)') (d_t(j,i),j=1,3) enddo - do i=1,2*nres + do i=0,2*nres-1 read(irest2,'(3e15.5)') (dc(j,i),j=1,3) enddo if(usampl) then @@ -2463,7 +2530,7 @@ c print *, "wchodze" call readi(afmcard,"END",afmend,0) call reada(afmcard,"FORCE",forceAFMconst,0.0d0) call reada(afmcard,"VEL",velAFMconst,0.0d0) - print *,'FORCE=' ,forceAFMconst +c print *,'FORCE=' ,forceAFMconst CCCC NOW PROPERTIES FOR AFM distafminit=0.0d0 do i=1,3 @@ -2974,10 +3041,11 @@ c & sigma_odl_temp(maxres,maxres,max_template) character*24 model_ki_dist, model_ki_angle character*500 controlcard integer ki,i,ii,j,k,l,ii_in_use(maxdim),i_tmp,idomain_tmp,irec, - & ik,iistart,iishift + & ik,iistart,nres_temp integer ilen external ilen - logical liiflag + logical liiflag,lfirst + integer i01,i10 c c FP - Nov. 2014 Temporary specifications for new vars c @@ -2987,7 +3055,8 @@ c double precision, dimension (max_template,maxres) :: rescore2 double precision, dimension (max_template,maxres) :: rescore3 double precision distal - character*24 pdbfile,tpl_k_rescore + character*24 tpl_k_rescore + character*256 pdbfile c ----------------------------------------------------------------- c Reading multiple PDB ref structures and calculation of retraints c not using pre-computed ones stored in files model_ki_{dist,angle} @@ -3010,15 +3079,17 @@ c Alternative: reading from input if(me.eq.king .or. .not. out1file .and. fg_rank.eq.0) & write(iout,*) 'START_FROM_MODELS works only with READ2SIGMA' start_from_model=.false. + iranconf=(indpdb.le.0) endif if(start_from_model .and. (me.eq.king .or. .not. out1file)) & write(iout,*) 'START_FROM_MODELS is ON' - if(start_from_model .and. rest) then - if(me.eq.king .or. .not. out1file .and. fg_rank.eq.0) then - write(iout,*) 'START_FROM_MODELS is OFF' - write(iout,*) 'remove restart keyword from input' - endif - endif +c if(start_from_model .and. rest) then +c if(me.eq.king .or. .not. out1file .and. fg_rank.eq.0) then +c write(iout,*) 'START_FROM_MODELS is OFF' +c write(iout,*) 'remove restart keyword from input' +c endif +c endif + if (start_from_model) nmodel_start=constr_homology if (homol_nset.gt.1)then call card_concat(controlcard) read(controlcard,*) (waga_homology(i),i=1,homol_nset) @@ -3064,6 +3135,7 @@ c do k=1,constr_homology read(inp,'(a)') pdbfile + pdbfiles_chomo(k)=pdbfile if(me.eq.king .or. .not. out1file) & write (iout,'(a,5x,a)') 'HOMOL: Opening PDB file', & pdbfile(:ilen(pdbfile)) @@ -3083,17 +3155,20 @@ c tpl_k_rescore="template"//kic2//".sco" unres_pdb=.false. + nres_temp=nres if (read2sigma) then call readpdb_template(k) else call readpdb endif + nres_chomo(k)=nres + nres=nres_temp c c Distance restraints c c ... --> odl(k,ii) C Copy the coordinates from reference coordinates (?) - do i=1,2*nres + do i=1,2*nres_chomo(k) do j=1,3 c(j,i)=cref(j,i) c write (iout,*) "c(",j,i,") =",c(j,i) @@ -3183,6 +3258,8 @@ c & constr_homology enddo lim_odl=ii endif +c write (iout,*) "Distance restraints set" +c call flush(iout) c c Theta, dihedral and SC retraints c @@ -3223,6 +3300,8 @@ c sigma_dih(k,i)=sigma_dih(k,i)*sigma_dih(k,i) enddo lim_dih=nct-nnt-2 endif +c write (iout,*) "Dihedral angle restraints set" +c call flush(iout) if (waga_theta.gt.0.0d0) then c open (ientin,file=tpl_k_sigma_theta,status='old') @@ -3258,6 +3337,8 @@ c rescore(k,i-2) ! right expression ? c sigma_theta(k,i)=sigma_theta(k,i)*sigma_theta(k,i) enddo endif +c write (iout,*) "Angle restraints set" +c call flush(iout) if (waga_d.gt.0.0d0) then c open (ientin,file=tpl_k_sigma_d,status='old') @@ -3293,51 +3374,66 @@ c read (ientin,*) sigma_d(k,i) ! 1st variant enddo endif enddo +c write (iout,*) "SC restraints set" +c call flush(iout) c c remove distance restraints not used in any model from the list c shift data in all arrays c +c write (iout,*) "waga_dist",waga_dist," nnt",nnt," nct",nct if (waga_dist.ne.0.0d0) then ii=0 liiflag=.true. + lfirst=.true. do i=nnt,nct-2 do j=i+2,nct ii=ii+1 - if (ii_in_use(ii).eq.0.and.liiflag) then +c if (idomain(k,i).eq.idomain(k,j).and.idomain(k,i).ne.0 +c & .and. distal.le.dist2_cut ) then +c write (iout,*) "i",i," j",j," ii",ii +c call flush(iout) + if (ii_in_use(ii).eq.0.and.liiflag.or. + & ii_in_use(ii).eq.1.and.liiflag.and.ii.eq.lim_odl) then liiflag=.false. - iistart=ii + i10=ii + if (lfirst) then + lfirst=.false. + iistart=ii + else + if(i10.eq.lim_odl) i10=i10+1 + do ki=0,i10-i01-1 + ires_homo(iistart+ki)=ires_homo(ki+i01) + jres_homo(iistart+ki)=jres_homo(ki+i01) + ii_in_use(iistart+ki)=ii_in_use(ki+i01) + do k=1,constr_homology + odl(k,iistart+ki)=odl(k,ki+i01) + sigma_odl(k,iistart+ki)=sigma_odl(k,ki+i01) + l_homo(k,iistart+ki)=l_homo(k,ki+i01) + enddo + enddo + iistart=iistart+i10-i01 + endif endif - if (ii_in_use(ii).ne.0.and..not.liiflag.or. - & .not.liiflag.and.ii.eq.lim_odl) then - if (ii.eq.lim_odl) then - iishift=ii-iistart+1 - else - iishift=ii-iistart - endif + if (ii_in_use(ii).ne.0.and..not.liiflag) then + i01=ii liiflag=.true. - do ki=iistart,lim_odl-iishift - ires_homo(ki)=ires_homo(ki+iishift) - jres_homo(ki)=jres_homo(ki+iishift) - ii_in_use(ki)=ii_in_use(ki+iishift) - do k=1,constr_homology - odl(k,ki)=odl(k,ki+iishift) - sigma_odl(k,ki)=sigma_odl(k,ki+iishift) - l_homo(k,ki)=l_homo(k,ki+iishift) - enddo - enddo - ii=ii-iishift - lim_odl=lim_odl-iishift endif enddo enddo + lim_odl=iistart-1 endif - +c write (iout,*) "Removing distances completed" +c call flush(iout) endif ! .not. klapaucjusz if (constr_homology.gt.0) call homology_partition +c write (iout,*) "After homology_partition" +c call flush(iout) if (constr_homology.gt.0) call init_int_table -c write (iout,*) "ithet_start =",ithet_start,"ithet_end =",ithet_end -c write (iout,*) "loc_start =",loc_start,"loc_end =",loc_end +c write (iout,*) "After init_int_table" +c call flush(iout) +c write (iout,*) "ithet_start =",ithet_start,"ithet_end =",ithet_end +c write (iout,*) "loc_start =",loc_start,"loc_end =",loc_end c c Print restraints c @@ -3535,6 +3631,7 @@ c---------------------------------------------------------------------- & ik,ll,ii,kk,iistart,iishift,lim_xx double precision distal logical lprn /.true./ + integer nres_temp integer ilen external ilen logical liiflag @@ -3543,7 +3640,8 @@ c double precision rescore_tmp,x12,y12,z12,rescore2_tmp double precision, dimension (max_template,maxres) :: rescore double precision, dimension (max_template,maxres) :: rescore2 - character*24 pdbfile,tpl_k_rescore + character*24 tpl_k_rescore + character*256 pdbfile c c For new homol impl @@ -3562,6 +3660,7 @@ c Read pdb files read(ientin,'(a)') pdbfile write (iout,'(a,5x,a)') 'KLAPAUCJUSZ: Opening PDB file', & pdbfile(:ilen(pdbfile)) + pdbfiles_chomo(k)=pdbfile open(ipdbin,file=pdbfile,status='old',err=33) goto 34 33 write (iout,'(a,5x,a)') 'Error opening PDB file', @@ -3569,7 +3668,10 @@ c Read pdb files stop 34 continue unres_pdb=.false. + nres_temp=nres call readpdb_template(k) + nres_chomo(k)=nres + nres=nres_temp do i=1,nres rescore(k,i)=0.2d0 rescore2(k,i)=1.0d0 @@ -3603,6 +3705,8 @@ c Distance restraints c c ... --> odl(k,ii) C Copy the coordinates from reference coordinates (?) + nres_temp=nres + nres=nres_chomo(k) do i=1,2*nres do j=1,3 c(j,i)=chomo(j,i,k) @@ -3615,6 +3719,7 @@ c write (iout,*) "c(",j,i,") =",c(j,i) thetaref(i)=theta(i) phiref(i)=phi(i) enddo + nres=nres_temp if (waga_dist.ne.0.0d0) then ii=0 do i = nnt,nct-2