X-Git-Url: http://mmka.chem.univ.gda.pl/gitweb/?a=blobdiff_plain;f=source%2Funres%2Fsrc_MD-M%2Freadrtns_CSA.F;h=c511fb5fd7c7d43f84b6194b41aed29a64ff0a66;hb=4a5964cdc6b84e3073a4155bf997640cf45b6993;hp=f944233c55145679de6db68f02272ea7df3e136b;hpb=3c5e1a8829ff84c0725642015445f4debd4ecc0a;p=unres.git diff --git a/source/unres/src_MD-M/readrtns_CSA.F b/source/unres/src_MD-M/readrtns_CSA.F index f944233..c511fb5 100644 --- a/source/unres/src_MD-M/readrtns_CSA.F +++ b/source/unres/src_MD-M/readrtns_CSA.F @@ -41,12 +41,18 @@ C Print restraint information #ifdef MPI if (.not. out1file .or. me.eq.king) then #endif - if (nhpb.gt.nss) - &write (iout,'(a,i5,a)') "The following",nhpb-nss, - & " distance constraints have been imposed" - do i=nss+1,nhpb - write (iout,'(3i6,f10.5)') i-nss,ihpb(i),jhpb(i),forcon(i) - enddo + if (nhpb.gt.nss) then + write (iout,'(/a,i5,a/4a5,2a8,3a10,a5)') + & "The following",nhpb-nss, + & " distance restraints have been imposed:", + & " Nr"," res1"," res2"," beta"," d1"," d2"," k"," V", + & " score"," type" + do i=nss+1,nhpb + write (iout,'(4i5,2f8.2,3f10.5,i5)')i-nss,ihpb(i),jhpb(i), + & ibecarb(i),dhpb(i),dhpb1(i),forcon(i),fordepth(i),xlscore(i), + & irestr_type(i) + enddo + endif #ifdef MPI endif #endif @@ -98,6 +104,13 @@ c print *,"Processor",me," fg_rank",fg_rank," out1file",out1file C Set up the time limit (caution! The time must be input in minutes!) read_cart=index(controlcard,'READ_CART').gt.0 call readi(controlcard,'CONSTR_DIST',constr_dist,0) + write (iout,*) "constr_dist",constr_dist + call readi(controlcard,'NSAXS',nsaxs,0) + call readi(controlcard,'SAXS_MODE',saxs_mode,0) + call reada(controlcard,'SCAL_RAD',scal_rad,1.0d0) + call reada(controlcard,'SAXS_CUTOFF',saxs_cutoff,1.0d0) + write (iout,*) "Number of SAXS restraints",NSAXS," SAXS_MODE", + & SAXS_MODE," SCAL_RAD",scal_rad,"SAXS_CUTOFF",saxs_cutoff call readi(controlcard,'CONSTR_HOMOL',constr_homology,0) call readi(controlcard,'SYM',symetr,1) call reada(controlcard,'TIMLIM',timlim,960.0D0) ! default 16 hours @@ -241,10 +254,10 @@ C endif if ((lipbufthick*2.0d0).gt.lipthick) &write(iout,*) "WARNING WRONG SIZE OF LIP AQ BUF" endif - write(iout,*) "bordliptop=",bordliptop - write(iout,*) "bordlipbot=",bordlipbot - write(iout,*) "bufliptop=",bufliptop - write(iout,*) "buflipbot=",buflipbot +c write(iout,*) "bordliptop=",bordliptop +c write(iout,*) "bordlipbot=",bordlipbot +c write(iout,*) "bufliptop=",bufliptop +c write(iout,*) "buflipbot=",buflipbot if (me.eq.king .or. .not.out1file ) @@ -619,6 +632,7 @@ C Read weights of the subsequent energy terms. call reada(weightcard,'DELT_CORR',delt_corr,0.5d0) call reada(weightcard,'TEMP0',temp0,300.0d0) call reada(weightcard,'WLT',wliptran,0.0D0) + call reada(weightcard,'WSAXS',wsaxs,1.0D0) if (index(weightcard,'SOFT').gt.0) ipot=6 C 12/1/95 Added weight for the multi-body term WCORR call reada(weightcard,'WCORRH',wcorr,1.0D0) @@ -642,6 +656,7 @@ C 12/1/95 Added weight for the multi-body term WCORR weights(17)=wbond weights(18)=scal14 weights(21)=wsccor + weights(25)=wsaxs if(me.eq.king.or..not.out1file) & write (iout,10) wsc,wscp,welec,wvdwpp,wbond,wang,wscloc,wtor, & wtor_d,wstrain,wel_loc,wcorr,wcorr5,wcorr6,wsccor,wturn3, @@ -803,12 +818,16 @@ c print *,'Finished reading pdb data' call gen_side(iti,theta(i+1),alph(i),omeg(i),fail) nsi=nsi+1 enddo +c AL 7/10/16 +c Calculalte only the coordinates of the current sidechain; no need to rebuild +c whole chain + call locate_side_chain(i) if(fail) write(iout,*)'Adding sidechain failed for res ', & i,' after ',nsi,' trials' endif enddo C 10/03/12 Adam: Recalculate coordinates with new side chain positions - call chainbuild +c call chainbuild endif endif if (indpdb.eq.0) then @@ -869,6 +888,7 @@ C 8/13/98 Set limits to generating the dihedral angles phibound(2,i)=pi enddo read (inp,*) ndih_constr + write (iout,*) "ndish_constr",ndih_constr if (ndih_constr.gt.0) then read (inp,*) ftors read (inp,*) (idih_constr(i),phi0(i),drange(i),i=1,ndih_constr) @@ -963,7 +983,7 @@ c---------------------- call MPI_Finalize(MPI_COMM_WORLD,IERROR) stop 'Error reading reference structure' #endif - 39 call chainbuild + 39 call chainbuild_extconf call setup_var czscore call geom_to_var(nvar,coord_exp_zs(1,1)) nstart_sup=nnt @@ -980,7 +1000,7 @@ czscore call geom_to_var(nvar,coord_exp_zs(1,1)) 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 if(me.eq.king.or..not.out1file) & write (iout,*) 'Contact order:',co @@ -998,6 +1018,8 @@ c write (iout,*) "constr_dist",constr_dist,nstart_sup,nsup enddo endif endif + write (iout,*) "calling read_saxs_consrtr",nsaxs + if (nsaxs.gt.0) call read_saxs_constr if (constr_homology.gt.0) then @@ -1082,7 +1104,10 @@ C initial geometry. enddo return else + write (iout,*) "Calling read_ang" call read_angles(inp,*36) + write (iout,*) "Calling chainbuild" + call chainbuild_extconf endif goto 37 36 write (iout,'(a)') 'Error reading angle file.' @@ -1107,6 +1132,53 @@ C initial geometry. omeg(i)=-120d0*deg2rad if (itype(i).le.0) omeg(i)=-omeg(i) enddo +c from old chainbuild +C +C Define the origin and orientation of the coordinate system and locate the +C first three CA's and SC(2). +C + call orig_frame +* +* Build the alpha-carbon chain. +* + do i=4,nres + call locate_next_res(i) + enddo +C +C First and last SC must coincide with the corresponding CA. +C + do j=1,3 + dc(j,nres+1)=0.0D0 + dc_norm(j,nres+1)=0.0D0 + dc(j,nres+nres)=0.0D0 + dc_norm(j,nres+nres)=0.0D0 + c(j,nres+1)=c(j,1) + c(j,nres+nres)=c(j,nres) + enddo +C +C Define the origin and orientation of the coordinate system and locate the +C first three CA's and SC(2). +C + call orig_frame +* +* Build the alpha-carbon chain. +* + do i=4,nres + call locate_next_res(i) + enddo +C +C First and last SC must coincide with the corresponding CA. +C + do j=1,3 + dc(j,nres+1)=0.0D0 + dc_norm(j,nres+1)=0.0D0 + dc(j,nres+nres)=0.0D0 + dc_norm(j,nres+nres)=0.0D0 + c(j,nres+1)=c(j,1) + c(j,nres+nres)=c(j,nres) + enddo + +c else if(me.eq.king.or..not.out1file) & write (iout,'(a)') 'Random-generated initial geometry.' @@ -1782,6 +1854,8 @@ c---------------------------------------------------------------------------- include 'DIMENSIONS' include 'COMMON.MINIM' include 'COMMON.IOUNITS' + include 'COMMON.CONTROL' + include 'COMMON.SETUP' character*80 ucase character*320 minimcard call card_concat(minimcard) @@ -1794,12 +1868,18 @@ c---------------------------------------------------------------------------- print_min_stat=min0(index(minimcard,'PRINT_MIN_STAT'),1) print_min_res=min0(index(minimcard,'PRINT_MIN_RES'),1) print_min_ini=min0(index(minimcard,'PRINT_MIN_INI'),1) +#ifdef MPI + if (.not. out1file .or. me.eq.king) then +#endif write (iout,'(/80(1h*)/20x,a/80(1h*))') & 'Options in energy minimization:' write (iout,'(4(a,i5),a,1pe14.5,a,1pe14.5)') & 'MaxMin:',MaxMin,' MaxFun:',MaxFun, & 'MinMin:',MinMin,' MinFun:',MinFun, & ' TolF:',TolF,' RTolF:',RTolF +#ifdef MPI + endif +#endif return end c---------------------------------------------------------------------------- @@ -2062,6 +2142,8 @@ C Get parameter filenames and open the parameter files. open (ielep,file=elename,status='old') call getenv_loc('SIDEPAR',sidename) open (isidep,file=sidename,status='old') + call getenv_loc('LIPTRANPAR',liptranname) + open (iliptranpar,file=liptranname,status='old') #else open(1,file=pref_orig(:ilen(pref_orig))//'.inp',status='old', & readonly) @@ -2093,7 +2175,7 @@ c print *,ithep_pdb," opened" call getenv_loc('SIDEPAR',sidename) open (isidep,file=sidename,status='old',readonly) call getenv_loc('LIPTRANPAR',liptranname) - open (iliptranpar,file=liptranname,status='old',action='read') + open (iliptranpar,file=liptranname,status='old',readonly) #ifndef CRYST_SC call getenv_loc('ROTPARPDB',rotname_pdb) open (irotam_pdb,file=rotname_pdb,status='old',action='read') @@ -2389,6 +2471,72 @@ CCCC NOW PROPERTIES FOR AFM end c------------------------------------------------------------------------------- + subroutine read_saxs_constr + implicit real*8 (a-h,o-z) + include 'DIMENSIONS' +#ifdef MPI + include 'mpif.h' +#endif + include 'COMMON.SETUP' + include 'COMMON.CONTROL' + include 'COMMON.CHAIN' + include 'COMMON.IOUNITS' + include 'COMMON.SBRIDGE' + double precision cm(3) +c read(inp,*) nsaxs + write (iout,*) "Calling read_saxs nsaxs",nsaxs + call flush(iout) + if (saxs_mode.eq.0) then +c SAXS distance distribution + do i=1,nsaxs + read(inp,*) distsaxs(i),Psaxs(i) + enddo + Cnorm = 0.0d0 + do i=1,nsaxs + Cnorm = Cnorm + Psaxs(i) + enddo + write (iout,*) "Cnorm",Cnorm + do i=1,nsaxs + Psaxs(i)=Psaxs(i)/Cnorm + enddo + write (iout,*) "Normalized distance distribution from SAXS" + do i=1,nsaxs + write (iout,'(f8.2,e15.5)') distsaxs(i),Psaxs(i) + enddo + Wsaxs0=0.0d0 + do i=1,nsaxs + Wsaxs0=Wsaxs0-Psaxs(i)*dlog(Psaxs(i)) + enddo + write (iout,*) "Wsaxs0",Wsaxs0 + else +c SAXS "spheres". + do i=1,nsaxs + read (inp,'(30x,3f8.3)') (Csaxs(j,i),j=1,3) + enddo + do j=1,3 + cm(j)=0.0d0 + enddo + do i=1,nsaxs + do j=1,3 + cm(j)=cm(j)+Csaxs(j,i) + enddo + enddo + do j=1,3 + cm(j)=cm(j)/nsaxs + enddo + do i=1,nsaxs + do j=1,3 + Csaxs(j,i)=Csaxs(j,i)-cm(j) + enddo + enddo + write (iout,*) "SAXS sphere coordinates" + do i=1,nsaxs + write (iout,'(i5,3f10.5)') i,(Csaxs(j,i),j=1,3) + enddo + endif + return + end +c------------------------------------------------------------------------------- subroutine read_dist_constr implicit real*8 (a-h,o-z) include 'DIMENSIONS' @@ -2403,18 +2551,40 @@ c------------------------------------------------------------------------------- integer ifrag_(2,100),ipair_(2,100) double precision wfrag_(100),wpair_(100) character*500 controlcard -c write (iout,*) "Calling read_dist_constr" + logical normalize,next + integer restr_type + double precision xlink(4,0:4) / +c a b c sigma + & 0.0d0,0.0d0,0.0d0,0.0d0, ! default, no xlink potential + & 0.00305218d0,9.46638d0,4.68901d0,4.74347d0, ! ZL + & 0.00214928d0,12.7517d0,0.00375009d0,6.13477d0, ! ADH + & 0.00184547d0,11.2678d0,0.00140292d0,7.00868d0, ! PDH + & 0.000161786d0,6.29273d0,4.40993d0,7.13956d0 / ! DSS +c print *, "WCHODZE" + write (iout,*) "Calling read_dist_constr" c write (iout,*) "nres",nres," nstart_sup",nstart_sup," nsup",nsup c call flush(iout) + next=.true. + + DO WHILE (next) + call card_concat(controlcard) + next = index(controlcard,"NEXT").gt.0 + call readi(controlcard,"RESTR_TYPE",restr_type,constr_dist) + write (iout,*) "restr_type",restr_type + call readi(controlcard,"NFRAG",nfrag_,0) call readi(controlcard,"NFRAG",nfrag_,0) call readi(controlcard,"NPAIR",npair_,0) call readi(controlcard,"NDIST",ndist_,0) call reada(controlcard,'DIST_CUT',dist_cut,5.0d0) + if (restr_type.eq.10) + & call reada(controlcard,'WBOLTZD',wboltzd,0.591d0) call multreadi(controlcard,"IFRAG",ifrag_(1,1),2*nfrag_,0) call multreadi(controlcard,"IPAIR",ipair_(1,1),2*npair_,0) call multreada(controlcard,"WFRAG",wfrag_(1),nfrag_,0.0d0) call multreada(controlcard,"WPAIR",wpair_(1),npair_,0.0d0) + normalize = index(controlcard,"NORMALIZE").gt.0 + write (iout,*) "WBOLTZD",wboltzd c write (iout,*) "NFRAG",nfrag_," NPAIR",npair_," NDIST",ndist_ c write (iout,*) "IFRAG" c do i=1,nfrag_ @@ -2424,46 +2594,38 @@ c write (iout,*) "IPAIR" c do i=1,npair_ c write (iout,*) i,ipair_(1,i),ipair_(2,i),wpair_(i) c enddo - if (.not.refstr .and. nfrag.gt.0) then - write (iout,*) - & "ERROR: no reference structure to compute distance restraints" - write (iout,*) - & "Restraints must be specified explicitly (NDIST=number)" - stop - endif - if (nfrag.lt.2 .and. npair.gt.0) then - write (iout,*) "ERROR: Less than 2 fragments specified", - & " but distance restraints between pairs requested" - stop - endif - call flush(iout) + if (nfrag_.gt.0) write (iout,*) + & "Distance restraints as generated from reference structure" do i=1,nfrag_ if (ifrag_(1,i).lt.nstart_sup) ifrag_(1,i)=nstart_sup if (ifrag_(2,i).gt.nstart_sup+nsup-1) & ifrag_(2,i)=nstart_sup+nsup-1 c write (iout,*) i,ifrag_(1,i),ifrag_(2,i),wfrag_(i) - call flush(iout) - if (wfrag_(i).gt.0.0d0) then +c call flush(iout) + if (wfrag_(i).eq.0.0d0) cycle do j=ifrag_(1,i),ifrag_(2,i)-1 do k=j+1,ifrag_(2,i) c write (iout,*) "j",j," k",k ddjk=dist(j,k) - if (constr_dist.eq.1) then - nhpb=nhpb+1 - ihpb(nhpb)=j - jhpb(nhpb)=k + if (restr_type.eq.1) then + nhpb=nhpb+1 + irestr_type(nhpb)=1 + ihpb(nhpb)=j + jhpb(nhpb)=k dhpb(nhpb)=ddjk - forcon(nhpb)=wfrag_(i) + forcon(nhpb)=wfrag_(i) else if (constr_dist.eq.2) then if (ddjk.le.dist_cut) then nhpb=nhpb+1 + irestr_type(nhpb)=1 ihpb(nhpb)=j jhpb(nhpb)=k dhpb(nhpb)=ddjk forcon(nhpb)=wfrag_(i) endif - else + else if (restr_type.eq.3) then nhpb=nhpb+1 + irestr_type(nhpb)=1 ihpb(nhpb)=j jhpb(nhpb)=k dhpb(nhpb)=ddjk @@ -2471,18 +2633,17 @@ c write (iout,*) "j",j," k",k endif #ifdef MPI if (.not.out1file .or. me.eq.king) - & write (iout,'(a,3i5,f8.2,1pe12.2)') "+dist.constr ", + & write (iout,'(a,3i5,f8.2,1pe12.2)') "+dist.restr ", & nhpb,ihpb(nhpb),jhpb(nhpb),dhpb(nhpb),forcon(nhpb) #else - write (iout,'(a,3i5,f8.2,1pe12.2)') "+dist.constr ", + write (iout,'(a,3i5,f8.2,1pe12.2)') "+dist.restr ", & nhpb,ihpb(nhpb),jhpb(nhpb),dhpb(nhpb),forcon(nhpb) #endif enddo enddo - endif enddo do i=1,npair_ - if (wpair_(i).gt.0.0d0) then + if (wpair_(i).eq.0.0d0) cycle ii = ipair_(1,i) jj = ipair_(2,i) if (ii.gt.jj) then @@ -2492,39 +2653,161 @@ c write (iout,*) "j",j," k",k endif do j=ifrag_(1,ii),ifrag_(2,ii) do k=ifrag_(1,jj),ifrag_(2,jj) - nhpb=nhpb+1 - ihpb(nhpb)=j - jhpb(nhpb)=k - forcon(nhpb)=wpair_(i) - dhpb(nhpb)=dist(j,k) + if (restr_type.eq.1) then + nhpb=nhpb+1 + irestr_type(nhpb)=1 + ihpb(nhpb)=j + jhpb(nhpb)=k + dhpb(nhpb)=ddjk + forcon(nhpb)=wfrag_(i) + else if (constr_dist.eq.2) then + if (ddjk.le.dist_cut) then + nhpb=nhpb+1 + irestr_type(nhpb)=1 + ihpb(nhpb)=j + jhpb(nhpb)=k + dhpb(nhpb)=ddjk + forcon(nhpb)=wfrag_(i) + endif + else if (restr_type.eq.3) then + nhpb=nhpb+1 + irestr_type(nhpb)=1 + ihpb(nhpb)=j + jhpb(nhpb)=k + dhpb(nhpb)=ddjk + forcon(nhpb)=wfrag_(i)*dexp(-0.5d0*(ddjk/dist_cut)**2) + endif #ifdef MPI if (.not.out1file .or. me.eq.king) - & write (iout,'(a,3i5,f8.2,f10.1)') "+dist.constr ", + & write (iout,'(a,3i5,f8.2,f10.1)') "+dist.restr ", & nhpb,ihpb(nhpb),jhpb(nhpb),dhpb(nhpb),forcon(nhpb) #else - write (iout,'(a,3i5,f8.2,f10.1)') "+dist.constr ", + write (iout,'(a,3i5,f8.2,f10.1)') "+dist.restr ", & nhpb,ihpb(nhpb),jhpb(nhpb),dhpb(nhpb),forcon(nhpb) #endif enddo enddo - endif enddo + +c print *,ndist_ + write (iout,*) "Distance restraints as read from input" do i=1,ndist_ - read (inp,*) ihpb(nhpb+1),jhpb(nhpb+1),forcon(nhpb+1) - if (forcon(nhpb+1).gt.0.0d0) then + if (restr_type.eq.11) then + read (inp,*) ihpb(nhpb+1),jhpb(nhpb+1),dhpb(nhpb+1), + & dhpb1(nhpb+1),ibecarb(i),forcon(nhpb+1),fordepth(nhpb+1) +c fordepth(nhpb+1)=fordepth(nhpb+1)/forcon(nhpb+1) + if (forcon(nhpb+1).le.0.0d0.or.fordepth(nhpb+1).le.0.0d0)cycle + nhpb=nhpb+1 + irestr_type(nhpb)=11 +#ifdef MPI + if (.not.out1file .or. me.eq.king) + & write (iout,'(a,4i5,2f8.2,2f10.5,i5)') "+dist.restr ", + & nhpb,ihpb(nhpb),jhpb(nhpb),ibecarb(nhpb),dhpb(nhpb), + & dhpb1(nhpb),forcon(nhpb),fordepth(nhpb),irestr_type(nhpb) +#else + write (iout,'(a,4i5,2f8.2,2f10.5,i5)') "+dist.restr ", + & nhpb,ihpb(nhpb),jhpb(nhpb),ibecarb(nhpb),dhpb(nhpb), + & dhpb1(nhpb),forcon(nhpb),fordepth(nhpb),irestr_type(nhpb) +#endif + if (ibecarb(nhpb).gt.0) then + ihpb(nhpb)=ihpb(nhpb)+nres + jhpb(nhpb)=jhpb(nhpb)+nres + endif + else if (constr_dist.eq.10) then +c Cross-lonk Markov-like potential + call card_concat(controlcard) + call readi(controlcard,"ILINK",ihpb(nhpb+1),0) + call readi(controlcard,"JLINK",jhpb(nhpb+1),0) + ibecarb(nhpb+1)=0 + if (index(controlcard,"BETA").gt.0) ibecarb(nhpb+1)=1 + if (ihpb(nhpb+1).eq.0 .or. jhpb(nhpb+1).eq.0) cycle + if (index(controlcard,"ZL").gt.0) then + link_type=1 + else if (index(controlcard,"ADH").gt.0) then + link_type=2 + else if (index(controlcard,"PDH").gt.0) then + link_type=3 + else if (index(controlcard,"DSS").gt.0) then + link_type=4 + else + link_type=0 + endif + call reada(controlcard,"AXLINK",dhpb(nhpb+1), + & xlink(1,link_type)) + call reada(controlcard,"BXLINK",dhpb1(nhpb+1), + & xlink(2,link_type)) + call reada(controlcard,"CXLINK",fordepth(nhpb+1), + & xlink(3,link_type)) + call reada(controlcard,"SIGMA",forcon(nhpb+1), + & xlink(4,link_type)) + call reada(controlcard,"SCORE",xlscore(nhpb+1),1.0d0) +c read (inp,*) ihpb(nhpb+1),jhpb(nhpb+1),ibecarb(nhpb+1), +c & dhpb(nhpb+1),dhpb1(nhpb+1),forcon(nhpb+1),fordepth(nhpb+1) + if (forcon(nhpb+1).le.0.0d0 .or. + & (dhpb(nhpb+1).eq.0 .and. dhpb1(nhpb+1).eq.0)) cycle nhpb=nhpb+1 - dhpb(nhpb)=dist(ihpb(nhpb),jhpb(nhpb)) + irestr_type(nhpb)=10 + if (ibecarb(nhpb).gt.0) then + ihpb(nhpb)=ihpb(nhpb)+nres + jhpb(nhpb)=jhpb(nhpb)+nres + endif #ifdef MPI if (.not.out1file .or. me.eq.king) - & write (iout,'(a,3i5,f8.2,f10.1)') "+dist.constr ", - & nhpb,ihpb(nhpb),jhpb(nhpb),dhpb(nhpb),forcon(nhpb) + & write (iout,'(a,4i5,2f8.2,3f10.5,i5)') "+dist.restr ", + & nhpb,ihpb(nhpb),jhpb(nhpb),ibecarb(nhpb),dhpb(nhpb), + & dhpb1(nhpb),forcon(nhpb),fordepth(nhpb),xlscore(nhpb), + & irestr_type(nhpb) #else - write (iout,'(a,3i5,f8.2,f10.1)') "+dist.constr ", - & nhpb,ihpb(nhpb),jhpb(nhpb),dhpb(nhpb),forcon(nhpb) + write (iout,'(a,4i5,2f8.2,3f10.5,i5)') "+dist.restr ", + & nhpb,ihpb(nhpb),jhpb(nhpb),ibecarb(nhpb),dhpb(nhpb), + & dhpb1(nhpb),forcon(nhpb),fordepth(nhpb),xlscore(nhpb), + & irestr_type(nhpb) #endif + else +C print *,"in else" + read (inp,*) ihpb(nhpb+1),jhpb(nhpb+1),dhpb(nhpb+1), + & dhpb1(nhpb+1),ibecarb(nhpb+1),forcon(nhpb+1) + if (forcon(nhpb+1).gt.0.0d0) then + nhpb=nhpb+1 + if (dhpb1(nhpb).eq.0.0d0) then + irestr_type(nhpb)=1 + else + irestr_type(nhpb)=2 + endif + if (ibecarb(nhpb).gt.0) then + ihpb(nhpb)=ihpb(nhpb)+nres + jhpb(nhpb)=jhpb(nhpb)+nres + endif + if (dhpb(nhpb).eq.0.0d0) + & dhpb(nhpb)=dist(ihpb(nhpb),jhpb(nhpb)) endif +#ifdef MPI + if (.not.out1file .or. me.eq.king) + & write (iout,'(a,4i5,f8.2,f10.1)') "+dist.restr ", + & nhpb,ihpb(nhpb),jhpb(nhpb),ibecarb(i),dhpb(nhpb),forcon(nhpb) +#else + write (iout,'(a,4i5,f8.2,f10.1)') "+dist.restr ", + & nhpb,ihpb(nhpb),jhpb(nhpb),ibecarb(i),dhpb(nhpb),forcon(nhpb) +#endif + endif +C read (inp,*) ihpb(nhpb+1),jhpb(nhpb+1),forcon(nhpb+1) +C if (forcon(nhpb+1).gt.0.0d0) then +C nhpb=nhpb+1 +C dhpb(nhpb)=dist(ihpb(nhpb),jhpb(nhpb)) enddo - call flush(iout) + + ENDDO ! next + + fordepthmax=0.0d0 + if (normalize) then + do i=nss+1,nhpb + if (irestr_type(i).eq.11.and.fordepth(i).gt.fordepthmax) + & fordepthmax=fordepth(i) + enddo + do i=nss+1,nhpb + if (irestr_type(i).eq.11) fordepth(i)=fordepth(i)/fordepthmax + enddo + endif return end c------------------------------------------------------------------------------- @@ -2542,6 +2825,7 @@ c------------------------------------------------------------------------------- include 'COMMON.MD' include 'COMMON.GEO' include 'COMMON.INTERACT' + include 'COMMON.NAMES' c c For new homol impl c @@ -2559,12 +2843,15 @@ c & sigma_odl_temp(maxres,maxres,max_template) logical lprn /.true./ integer ilen external ilen + logical liiflag c c FP - Nov. 2014 Temporary specifications for new vars c - double precision rescore_tmp,x12,y12,z12,rescore2_tmp + double precision rescore_tmp,x12,y12,z12,rescore2_tmp, + & rescore3_tmp double precision, dimension (max_template,maxres) :: rescore double precision, dimension (max_template,maxres) :: rescore2 + double precision, dimension (max_template,maxres) :: rescore3 character*24 pdbfile,tpl_k_rescore c ----------------------------------------------------------------- c Reading multiple PDB ref structures and calculation of retraints @@ -2585,13 +2872,17 @@ c Alternative: reading from input read2sigma=(index(controlcard,'READ2SIGMA').gt.0) start_from_model=(index(controlcard,'START_FROM_MODELS').gt.0) if(.not.read2sigma.and.start_from_model) then - write(iout,*) 'START_FROM_MODELS works only with READ2SIGMA' + 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. endif - if(start_from_model) write(iout,*) 'START_FROM_MODELS is ON' + 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 - write(iout,*) 'START_FROM_MODELS is OFF' - write(iout,*) 'remove restart keyword from input' + 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 if (homol_nset.gt.1)then call card_concat(controlcard) @@ -2615,12 +2906,7 @@ cd call flush(iout) lim_odl=0 lim_dih=0 c -c New -c - lim_theta=0 - lim_xx=0 -c - write(iout,*) 'nnt=',nnt,'nct=',nct +c write(iout,*) 'nnt=',nnt,'nct=',nct c do i = nnt,nct do k=1,constr_homology @@ -2639,11 +2925,8 @@ c do k=1,constr_homology read(inp,'(a)') pdbfile -c Next stament causes error upon compilation (?) -c if(me.eq.king.or. .not. out1file) -c write (iout,'(2a)') 'PDB data will be read from file ', -c & pdbfile(:ilen(pdbfile)) - write (iout,'(a,5x,a)') 'HOMOL: Opening PDB file', + if(me.eq.king .or. .not. out1file) + & write (iout,'(a,5x,a)') 'HOMOL: Opening PDB file', & pdbfile(:ilen(pdbfile)) open(ipdbin,file=pdbfile,status='old',err=33) goto 34 @@ -2683,14 +2966,19 @@ c c write(iout,*) "tpl_k_rescore - ",tpl_k_rescore open (ientin,file=tpl_k_rescore,status='old') if (nnt.gt.1) rescore(k,1)=0.0d0 - do irec=nnt,maxdim ! loop for reading res sim + do irec=nnt,nct ! loop for reading res sim if (read2sigma) then read (ientin,*,end=1401) i_tmp,rescore2_tmp,rescore_tmp, - & idomain_tmp + & rescore3_tmp,idomain_tmp i_tmp=i_tmp+nnt-1 idomain(k,i_tmp)=idomain_tmp rescore(k,i_tmp)=rescore_tmp rescore2(k,i_tmp)=rescore2_tmp + rescore3(k,i_tmp)=rescore3_tmp + if (.not. out1file .or. me.eq.king) + & write(iout,'(a7,i5,3f10.5,i5)') "rescore", + & i_tmp,rescore2_tmp,rescore_tmp, + & rescore3_tmp,idomain_tmp else idomain(k,irec)=1 read (ientin,*,end=1401) rescore_tmp @@ -2790,7 +3078,8 @@ c write (iout,'(i5,10(2f8.2,4x))') i,sigma_dih(k,i) c sigma_dih(k,i)=hmscore(k)*rescore(k,i)*rescore(k,i-1)* c rescore(k,i-2)*rescore(k,i-3) ! right expression ? c Instead of res sim other local measure of b/b str reliability possible - sigma_dih(k,i)=1.0d0/(sigma_dih(k,i)*sigma_dih(k,i)) + if (sigma_dih(k,i).ne.0) + & sigma_dih(k,i)=1.0d0/(sigma_dih(k,i)*sigma_dih(k,i)) c sigma_dih(k,i)=sigma_dih(k,i)*sigma_dih(k,i) enddo lim_dih=nct-nnt-2 @@ -2822,14 +3111,14 @@ c read (ientin,*) sigma_theta(k,i) ! 1st variant sigma_theta(k,i)=(rescore(k,i)+rescore(k,i-1)+ & rescore(k,i-2))/3.0 c if (read2sigma) sigma_theta(k,i)=sigma_theta(k,i)/3.0 - sigma_theta(k,i)=1.0d0/(sigma_theta(k,i)*sigma_theta(k,i)) + if (sigma_theta(k,i).ne.0) + & sigma_theta(k,i)=1.0d0/(sigma_theta(k,i)*sigma_theta(k,i)) c sigma_theta(k,i)=hmscore(k)*rescore(k,i)*rescore(k,i-1)* c rescore(k,i-2) ! right expression ? c sigma_theta(k,i)=sigma_theta(k,i)*sigma_theta(k,i) enddo endif - lim_theta=nct-nnt-1 if (waga_d.gt.0.0d0) then c open (ientin,file=tpl_k_sigma_d,status='old') @@ -2855,15 +3144,14 @@ c write (iout,*) "xxtpl(",k,i,") =",xxtpl(k,i) c write (iout,*) "yytpl(",k,i,") =",yytpl(k,i) c write (iout,*) "zztpl(",k,i,") =",zztpl(k,i) c write(iout,*) "rescore(",k,i,") =",rescore(k,i) - sigma_d(k,i)=rescore(k,i) ! right expression ? - sigma_d(k,i)=1.0d0/(sigma_d(k,i)*sigma_d(k,i)) + sigma_d(k,i)=rescore3(k,i) ! right expression ? + if (sigma_d(k,i).ne.0) + & sigma_d(k,i)=1.0d0/(sigma_d(k,i)*sigma_d(k,i)) c sigma_d(k,i)=hmscore(k)*rescore(k,i) ! right expression ? c sigma_d(k,i)=sigma_d(k,i)*sigma_d(k,i) c read (ientin,*) sigma_d(k,i) ! 1st variant - if (i-nnt+1.gt.lim_xx) lim_xx=i-nnt+1 ! right? enddo - lim_xx=nct-nnt+1 endif enddo c @@ -2872,30 +3160,40 @@ c shift data in all arrays c if (waga_dist.ne.0.0d0) then ii=0 + liiflag=.true. do i=nnt,nct-2 do j=i+2,nct ii=ii+1 - if (ii_in_use(ii).eq.0) then - do ki=ii,lim_odl-1 - ires_homo(ki)=ires_homo(ki+1) - jres_homo(ki)=jres_homo(ki+1) - ii_in_use(ki)=ii_in_use(ki+1) + if (ii_in_use(ii).eq.0.and.liiflag) then + liiflag=.false. + iistart=ii + 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 + 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+1) - sigma_odl(k,ki)=sigma_odl(k,ki+1) - l_homo(k,ki)=l_homo(k,ki+1) + 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-1 - lim_odl=lim_odl-1 + ii=ii-iishift + lim_odl=lim_odl-iishift endif enddo enddo endif if (constr_homology.gt.0) call homology_partition if (constr_homology.gt.0) call init_int_table -cd write (iout,*) "homology_partition: lim_theta= ",lim_theta, -cd & "lim_xx=",lim_xx c write (iout,*) "ithet_start =",ithet_start,"ithet_end =",ithet_end c write (iout,*) "loc_start =",loc_start,"loc_end =",loc_end c @@ -2912,17 +3210,19 @@ cd write(iout,*) "waga_theta",waga_theta,"waga_d",waga_d & ki=1,constr_homology) enddo write (iout,*) "Dihedral angle restraints from templates" - do i=nnt+3,lim_dih - write (iout,'(i5,100(2f8.2,4x))') i,(rad2deg*dih(ki,i), + do i=nnt+3,nct + write (iout,'(i5,a4,100(2f8.2,4x))') i,restyp(itype(i)), + & (rad2deg*dih(ki,i), & rad2deg/dsqrt(sigma_dih(ki,i)),ki=1,constr_homology) enddo write (iout,*) "Virtual-bond angle restraints from templates" - do i=nnt+2,lim_theta - write (iout,'(i5,100(2f8.2,4x))') i,(rad2deg*thetatpl(ki,i), + do i=nnt+2,nct + write (iout,'(i5,a4,100(2f8.2,4x))') i,restyp(itype(i)), + & (rad2deg*thetatpl(ki,i), & rad2deg/dsqrt(sigma_theta(ki,i)),ki=1,constr_homology) enddo write (iout,*) "SC restraints from templates" - do i=nnt,lim_xx + do i=nnt,nct write(iout,'(i5,100(4f8.2,4x))') i, & (xxtpl(ki,i),yytpl(ki,i),zztpl(ki,i), & 1.0d0/dsqrt(sigma_d(ki,i)),ki=1,constr_homology)