X-Git-Url: http://mmka.chem.univ.gda.pl/gitweb/?p=unres.git;a=blobdiff_plain;f=source%2Funres%2Fsrc_CSA_DiL%2Ftest.F;fp=source%2Funres%2Fsrc_CSA_DiL%2Ftest.F;h=0000000000000000000000000000000000000000;hp=a065af91867bb7605cb74945ab82dd50bf6075db;hb=de4bc5453ea46e111d936cb85e1758ed21c08fcd;hpb=b75425747e3e2b448ca5e0ef8367712e1f339124 diff --git a/source/unres/src_CSA_DiL/test.F b/source/unres/src_CSA_DiL/test.F deleted file mode 100644 index a065af9..0000000 --- a/source/unres/src_CSA_DiL/test.F +++ /dev/null @@ -1,2800 +0,0 @@ - subroutine test - implicit real*8 (a-h,o-z) - include 'DIMENSIONS' -#ifdef MPI - include 'mpif.h' -#endif - include 'COMMON.GEO' - include 'COMMON.VAR' - include 'COMMON.INTERACT' - include 'COMMON.IOUNITS' - include 'COMMON.DISTFIT' - include 'COMMON.SBRIDGE' - include 'COMMON.CONTROL' - include 'COMMON.FFIELD' - include 'COMMON.MINIM' - include 'COMMON.CHAIN' - double precision time0,time1 - double precision energy(0:n_ene),ee - double precision var(maxvar),var1(maxvar) - integer j1,j2 - logical debug,accepted - debug=.true. - - - call geom_to_var(nvar,var1) - call chainbuild - call etotal(energy(0)) - etot=energy(0) - call rmsd(rms) - write(iout,*) 'etot=',0,etot,rms - call secondary2(.false.) - - call write_pdb(0,'first structure',etot) - - j1=13 - j2=21 - da=180.0*deg2rad - - - - temp=3000.0d0 - betbol=1.0D0/(1.9858D-3*temp) - jr=iran_num(j1,j2) - d=ran_number(-pi,pi) -c phi(jr)=pinorm(phi(jr)+d) - call chainbuild - call etotal(energy(0)) - etot0=energy(0) - call rmsd(rms) - write(iout,*) 'etot=',1,etot0,rms - call write_pdb(1,'perturb structure',etot0) - - do i=2,500,2 - jr=iran_num(j1,j2) - d=ran_number(-da,da) - phiold=phi(jr) - phi(jr)=pinorm(phi(jr)+d) - call chainbuild - call etotal(energy(0)) - etot=energy(0) - - if (etot.lt.etot0) then - accepted=.true. - else - accepted=.false. - xxr=ran_number(0.0D0,1.0D0) - xxh=betbol*(etot-etot0) - if (xxh.lt.50.0D0) then - xxh=dexp(-xxh) - if (xxh.gt.xxr) accepted=.true. - endif - endif - accepted=.true. -c print *,etot0,etot,accepted - if (accepted) then - etot0=etot - call rmsd(rms) - write(iout,*) 'etot=',i,etot,rms - call write_pdb(i,'MC structure',etot) -c minimize -c call geom_to_var(nvar,var1) - call sc_move(2,nres-1,1,10d0,nft_sc,etot) - call geom_to_var(nvar,var) - call minimize(etot,var,iretcode,nfun) - write(iout,*)'SUMSL return code is',iretcode,' eval ',nfun - call var_to_geom(nvar,var) - call chainbuild - call rmsd(rms) - write(iout,*) 'etot mcm=',i,etot,rms - call write_pdb(i+1,'MCM structure',etot) - call var_to_geom(nvar,var1) -c -------- - else - phi(jr)=phiold - endif - enddo - -c minimize -c call sc_move(2,nres-1,1,10d0,nft_sc,etot) -c call geom_to_var(nvar,var) -c -c call chainbuild -c call write_pdb(998 ,'sc min',etot) -c -c call minimize(etot,var,iretcode,nfun) -c write(iout,*)'------------------------------------------------' -c write(iout,*)'SUMSL return code is',iretcode,' eval ',nfun -c -c call var_to_geom(nvar,var) -c call chainbuild -c call write_pdb(999,'full min',etot) - - - return - end - - - subroutine test_n16 - implicit real*8 (a-h,o-z) - include 'DIMENSIONS' -#ifdef MPI - include 'mpif.h' -#endif - include 'COMMON.GEO' - include 'COMMON.VAR' - include 'COMMON.INTERACT' - include 'COMMON.IOUNITS' - include 'COMMON.DISTFIT' - include 'COMMON.SBRIDGE' - include 'COMMON.CONTROL' - include 'COMMON.FFIELD' - include 'COMMON.MINIM' - include 'COMMON.CHAIN' - double precision time0,time1 - double precision energy(0:n_ene),ee - double precision var(maxvar),var1(maxvar) - integer jdata(5) - logical debug - debug=.true. - -c - call geom_to_var(nvar,var1) - call chainbuild - call etotal(energy(0)) - etot=energy(0) - write(iout,*) nnt,nct,etot - call write_pdb(1,'first structure',etot) - call secondary2(.true.) - - do i=1,4 - jdata(i)=bfrag(i,2) - enddo - - DO ij=1,4 - ieval=0 - jdata(5)=ij - call var_to_geom(nvar,var1) - write(iout,*) 'N16 test',(jdata(i),i=1,5) - call beta_slide(jdata(1),jdata(2),jdata(3),jdata(4),jdata(5) - & ,ieval,ij) - call geom_to_var(nvar,var) - - if (minim) then -#ifdef MPI - time0=MPI_WTIME() -#else - time0=tcpu() -#endif - call minimize(etot,var,iretcode,nfun) - write(iout,*)'------------------------------------------------' - write(iout,*)'SUMSL return code is',iretcode,' eval ',nfun, - & '+ DIST eval',ieval - -#ifdef MPI - time1=MPI_WTIME() -#else - time1=tcpu() -#endif - write (iout,'(a,f6.2,f8.2,a)')' Time for full min.',time1-time0, - & nfun/(time1-time0),' eval/s' - - call var_to_geom(nvar,var) - call chainbuild - call write_pdb(ij*100+99,'full min',etot) - endif - - - ENDDO - - return - end - - - subroutine test_local - implicit real*8 (a-h,o-z) - include 'DIMENSIONS' - include 'COMMON.GEO' - include 'COMMON.VAR' - include 'COMMON.INTERACT' - include 'COMMON.IOUNITS' - double precision time0,time1 - double precision energy(0:n_ene),ee - double precision varia(maxvar) -c - call chainbuild -c call geom_to_var(nvar,varia) - call write_pdb(1,'first structure',0d0) - - call etotal(energy(0)) - etot=energy(0) - write(iout,*) nnt,nct,etot - - write(iout,*) 'calling sc_move' - call sc_move(nnt,nct,5,10d0,nft_sc,etot) - write(iout,*) nft_sc,etot - call write_pdb(2,'second structure',etot) - - write(iout,*) 'calling local_move' - call local_move_init(.false.) - call local_move(24,29,20d0,50d0) - call chainbuild - call write_pdb(3,'third structure',etot) - - write(iout,*) 'calling sc_move' - call sc_move(24,29,5,10d0,nft_sc,etot) - write(iout,*) nft_sc,etot - call write_pdb(2,'last structure',etot) - - - return - end - - subroutine test_sc - implicit real*8 (a-h,o-z) - include 'DIMENSIONS' - include 'COMMON.GEO' - include 'COMMON.VAR' - include 'COMMON.INTERACT' - include 'COMMON.IOUNITS' - double precision time0,time1 - double precision energy(0:n_ene),ee - double precision varia(maxvar) -c - call chainbuild -c call geom_to_var(nvar,varia) - call write_pdb(1,'first structure',0d0) - - call etotal(energy(0)) - etot=energy(0) - write(iout,*) nnt,nct,etot - - write(iout,*) 'calling sc_move' - - call sc_move(nnt,nct,5,10d0,nft_sc,etot) - write(iout,*) nft_sc,etot - call write_pdb(2,'second structure',etot) - - write(iout,*) 'calling sc_move 2nd time' - - call sc_move(nnt,nct,5,1d0,nft_sc,etot) - write(iout,*) nft_sc,etot - call write_pdb(3,'last structure',etot) - return - end -c-------------------------------------------------------- - subroutine bgrow(bstrand,nbstrand,in,ind,new) - implicit real*8 (a-h,o-z) - include 'DIMENSIONS' - include 'COMMON.CHAIN' - integer bstrand(maxres/3,6) - - ishift=iabs(bstrand(in,ind+4)-new) - - print *,'bgrow',bstrand(in,ind+4),new,ishift - - bstrand(in,ind)=new - - if(ind.eq.1)then - bstrand(nbstrand,5)=bstrand(nbstrand,1) - do i=1,nbstrand-1 - IF (bstrand(nbstrand,3).eq.bstrand(i,3)) THEN - if (bstrand(i,5).lt.bstrand(i,6)) then - bstrand(i,5)=bstrand(i,5)-ishift - else - bstrand(i,5)=bstrand(i,5)+ishift - endif - ENDIF - enddo - else - bstrand(nbstrand,6)=bstrand(nbstrand,2) - do i=1,nbstrand-1 - IF (bstrand(nbstrand,3).eq.bstrand(i,3)) THEN - if (bstrand(i,6).lt.bstrand(i,5)) then - bstrand(i,6)=bstrand(i,6)-ishift - else - bstrand(i,6)=bstrand(i,6)+ishift - endif - ENDIF - enddo - endif - - - return - end - - -c------------------------------------------ - subroutine test11 - implicit real*8 (a-h,o-z) - include 'DIMENSIONS' -#ifdef MPI - include 'mpif.h' -#endif - include 'COMMON.GEO' - include 'COMMON.CHAIN' - include 'COMMON.IOUNITS' - include 'COMMON.VAR' - include 'COMMON.CONTROL' - include 'COMMON.SBRIDGE' - include 'COMMON.FFIELD' - include 'COMMON.MINIM' -c - include 'COMMON.DISTFIT' - integer if(20,maxres),nif,ifa(20) - integer ibc(0:maxres,0:maxres),istrand(20) - integer ibd(maxres),ifb(10,2),nifb,lifb(10),lifb0 - integer itmp(20,maxres) - double precision time0,time1 - double precision energy(0:n_ene),ee - double precision varia(maxvar),vorg(maxvar) -c - logical debug,ltest,usedbfrag(maxres/3) - character*50 linia -c - integer betasheet(maxres),ibetasheet(maxres),nbetasheet - integer bstrand(maxres/3,6),nbstrand - -c------------------------ - - debug=.true. -c------------------------ - nbstrand=0 - nbetasheet=0 - do i=1,nres - betasheet(i)=0 - ibetasheet(i)=0 - enddo - call geom_to_var(nvar,vorg) - call secondary2(debug) - - if (nbfrag.le.1) return - - do i=1,nbfrag - usedbfrag(i)=.false. - enddo - - - nbetasheet=nbetasheet+1 - nbstrand=2 - bstrand(1,1)=bfrag(1,1) - bstrand(1,2)=bfrag(2,1) - bstrand(1,3)=nbetasheet - bstrand(1,4)=1 - bstrand(1,5)=bfrag(1,1) - bstrand(1,6)=bfrag(2,1) - do i=bfrag(1,1),bfrag(2,1) - betasheet(i)=nbetasheet - ibetasheet(i)=1 - enddo -c - bstrand(2,1)=bfrag(3,1) - bstrand(2,2)=bfrag(4,1) - bstrand(2,3)=nbetasheet - bstrand(2,5)=bfrag(3,1) - bstrand(2,6)=bfrag(4,1) - - if (bfrag(3,1).le.bfrag(4,1)) then - bstrand(2,4)=2 - do i=bfrag(3,1),bfrag(4,1) - betasheet(i)=nbetasheet - ibetasheet(i)=2 - enddo - else - bstrand(2,4)=-2 - do i=bfrag(4,1),bfrag(3,1) - betasheet(i)=nbetasheet - ibetasheet(i)=2 - enddo - endif - - iused_nbfrag=1 - - do while (iused_nbfrag.ne.nbfrag) - - do j=2,nbfrag - - IF (.not.usedbfrag(j)) THEN - - write (*,*) j,(bfrag(i,j),i=1,4) - do jk=6,1,-1 - write (*,'(i4,a3,10i4)') jk,'B',(bstrand(i,jk),i=1,nbstrand) - enddo - write (*,*) '------------------' - - - if (bfrag(3,j).le.bfrag(4,j)) then - do i=bfrag(3,j),bfrag(4,j) - if(betasheet(i).eq.nbetasheet) then - in=ibetasheet(i) - do k=bfrag(3,j),bfrag(4,j) - betasheet(k)=nbetasheet - ibetasheet(k)=in - enddo - nbstrand=nbstrand+1 - usedbfrag(j)=.true. - iused_nbfrag=iused_nbfrag+1 - do k=bfrag(1,j),bfrag(2,j) - betasheet(k)=nbetasheet - ibetasheet(k)=nbstrand - enddo - if (bstrand(in,4).lt.0) then - bstrand(nbstrand,1)=bfrag(2,j) - bstrand(nbstrand,2)=bfrag(1,j) - bstrand(nbstrand,3)=nbetasheet - bstrand(nbstrand,4)=-nbstrand - bstrand(nbstrand,5)=bstrand(nbstrand,1) - bstrand(nbstrand,6)=bstrand(nbstrand,2) - if(bstrand(in,1).lt.bfrag(4,j)) then - call bgrow(bstrand,nbstrand,in,1,bfrag(4,j)) - else - bstrand(nbstrand,5)=bstrand(nbstrand,5)+ - & (bstrand(in,5)-bfrag(4,j)) - endif - if(bstrand(in,2).gt.bfrag(3,j)) then - call bgrow(bstrand,nbstrand,in,2,bfrag(3,j)) - else - bstrand(nbstrand,6)=bstrand(nbstrand,6)- - & (-bstrand(in,6)+bfrag(3,j)) - endif - else - bstrand(nbstrand,1)=bfrag(1,j) - bstrand(nbstrand,2)=bfrag(2,j) - bstrand(nbstrand,3)=nbetasheet - bstrand(nbstrand,4)=nbstrand - bstrand(nbstrand,5)=bstrand(nbstrand,1) - bstrand(nbstrand,6)=bstrand(nbstrand,2) - if(bstrand(in,1).gt.bfrag(3,j)) then - call bgrow(bstrand,nbstrand,in,1,bfrag(3,j)) - else - bstrand(nbstrand,5)=bstrand(nbstrand,5)- - & (-bstrand(in,5)+bfrag(3,j)) - endif - if(bstrand(in,2).lt.bfrag(4,j)) then - call bgrow(bstrand,nbstrand,in,2,bfrag(4,j)) - else - bstrand(nbstrand,6)=bstrand(nbstrand,6)+ - & (bstrand(in,6)-bfrag(4,j)) - endif - endif - goto 11 - endif - if(betasheet(bfrag(1,j)+i-bfrag(3,j)).eq.nbetasheet) then - in=ibetasheet(bfrag(1,j)+i-bfrag(3,j)) - do k=bfrag(1,j),bfrag(2,j) - betasheet(k)=nbetasheet - ibetasheet(k)=in - enddo - nbstrand=nbstrand+1 - usedbfrag(j)=.true. - iused_nbfrag=iused_nbfrag+1 - do k=bfrag(3,1),bfrag(4,1) - betasheet(k)=nbetasheet - ibetasheet(k)=nbstrand - enddo - if (bstrand(in,4).lt.0) then - bstrand(nbstrand,1)=bfrag(4,j) - bstrand(nbstrand,2)=bfrag(3,j) - bstrand(nbstrand,3)=nbetasheet - bstrand(nbstrand,4)=-nbstrand - bstrand(nbstrand,5)=bstrand(nbstrand,1) - bstrand(nbstrand,6)=bstrand(nbstrand,2) - if(bstrand(in,1).lt.bfrag(2,j)) then - call bgrow(bstrand,nbstrand,in,1,bfrag(2,j)) - else - bstrand(nbstrand,5)=bstrand(nbstrand,5)+ - & (bstrand(in,5)-bfrag(2,j)) - endif - if(bstrand(in,2).gt.bfrag(1,j)) then - call bgrow(bstrand,nbstrand,in,2,bfrag(1,j)) - else - bstrand(nbstrand,6)=bstrand(nbstrand,6)- - & (-bstrand(in,6)+bfrag(1,j)) - endif - else - bstrand(nbstrand,1)=bfrag(3,j) - bstrand(nbstrand,2)=bfrag(4,j) - bstrand(nbstrand,3)=nbetasheet - bstrand(nbstrand,4)=nbstrand - bstrand(nbstrand,5)=bstrand(nbstrand,1) - bstrand(nbstrand,6)=bstrand(nbstrand,2) - if(bstrand(in,1).gt.bfrag(1,j)) then - call bgrow(bstrand,nbstrand,in,1,bfrag(1,j)) - else - bstrand(nbstrand,5)=bstrand(nbstrand,5)- - & (-bstrand(in,5)+bfrag(1,j)) - endif - if(bstrand(in,2).lt.bfrag(2,j)) then - call bgrow(bstrand,nbstrand,in,2,bfrag(2,j)) - else - bstrand(nbstrand,6)=bstrand(nbstrand,6)+ - & (bstrand(in,6)-bfrag(2,j)) - endif - endif - goto 11 - endif - enddo - else - do i=bfrag(4,j),bfrag(3,j) - if(betasheet(i).eq.nbetasheet) then - in=ibetasheet(i) - do k=bfrag(4,j),bfrag(3,j) - betasheet(k)=nbetasheet - ibetasheet(k)=in - enddo - nbstrand=nbstrand+1 - usedbfrag(j)=.true. - iused_nbfrag=iused_nbfrag+1 - do k=bfrag(1,j),bfrag(2,j) - betasheet(k)=nbetasheet - ibetasheet(k)=nbstrand - enddo - if (bstrand(in,4).lt.0) then - bstrand(nbstrand,1)=bfrag(1,j) - bstrand(nbstrand,2)=bfrag(2,j) - bstrand(nbstrand,3)=nbetasheet - bstrand(nbstrand,4)=nbstrand - bstrand(nbstrand,5)=bstrand(nbstrand,1) - bstrand(nbstrand,6)=bstrand(nbstrand,2) - if(bstrand(in,1).lt.bfrag(3,j)) then - call bgrow(bstrand,nbstrand,in,1,bfrag(3,j)) - else - bstrand(nbstrand,5)=bstrand(nbstrand,5)- - & (bstrand(in,5)-bfrag(3,j)) - endif - if(bstrand(in,2).gt.bfrag(4,j)) then - call bgrow(bstrand,nbstrand,in,2,bfrag(4,j)) - else - bstrand(nbstrand,6)=bstrand(nbstrand,6)+ - & (-bstrand(in,6)+bfrag(4,j)) - endif - else - bstrand(nbstrand,1)=bfrag(2,j) - bstrand(nbstrand,2)=bfrag(1,j) - bstrand(nbstrand,3)=nbetasheet - bstrand(nbstrand,4)=-nbstrand - bstrand(nbstrand,5)=bstrand(nbstrand,1) - bstrand(nbstrand,6)=bstrand(nbstrand,2) - if(bstrand(in,1).gt.bfrag(4,j)) then - call bgrow(bstrand,nbstrand,in,1,bfrag(4,j)) - else - bstrand(nbstrand,5)=bstrand(nbstrand,5)+ - & (-bstrand(in,5)+bfrag(4,j)) - endif - if(bstrand(in,2).lt.bfrag(3,j)) then - call bgrow(bstrand,nbstrand,in,2,bfrag(3,j)) - else - bstrand(nbstrand,6)=bstrand(nbstrand,6)- - & (bstrand(in,6)-bfrag(3,j)) - endif - endif - goto 11 - endif - if(betasheet(bfrag(2,j)-i+bfrag(4,j)).eq.nbetasheet) then - in=ibetasheet(bfrag(2,j)-i+bfrag(4,j)) - do k=bfrag(1,j),bfrag(2,j) - betasheet(k)=nbetasheet - ibetasheet(k)=in - enddo - nbstrand=nbstrand+1 - usedbfrag(j)=.true. - iused_nbfrag=iused_nbfrag+1 - do k=bfrag(4,j),bfrag(3,j) - betasheet(k)=nbetasheet - ibetasheet(k)=nbstrand - enddo - if (bstrand(in,4).lt.0) then - bstrand(nbstrand,1)=bfrag(4,j) - bstrand(nbstrand,2)=bfrag(3,j) - bstrand(nbstrand,3)=nbetasheet - bstrand(nbstrand,4)=nbstrand - bstrand(nbstrand,5)=bstrand(nbstrand,1) - bstrand(nbstrand,6)=bstrand(nbstrand,2) - if(bstrand(in,1).lt.bfrag(2,j)) then - call bgrow(bstrand,nbstrand,in,1,bfrag(2,j)) - else - bstrand(nbstrand,5)=bstrand(nbstrand,5)- - & (bstrand(in,5)-bfrag(2,j)) - endif - if(bstrand(in,2).gt.bfrag(1,j)) then - call bgrow(bstrand,nbstrand,in,2,bfrag(1,j)) - else - bstrand(nbstrand,6)=bstrand(nbstrand,6)+ - & (-bstrand(in,6)+bfrag(1,j)) - endif - else - bstrand(nbstrand,1)=bfrag(3,j) - bstrand(nbstrand,2)=bfrag(4,j) - bstrand(nbstrand,3)=nbetasheet - bstrand(nbstrand,4)=-nbstrand - bstrand(nbstrand,5)=bstrand(nbstrand,1) - bstrand(nbstrand,6)=bstrand(nbstrand,2) - if(bstrand(in,1).gt.bfrag(1,j)) then - call bgrow(bstrand,nbstrand,in,1,bfrag(1,j)) - else - bstrand(nbstrand,5)=bstrand(nbstrand,5)+ - & (-bstrand(in,5)+bfrag(1,j)) - endif - if(bstrand(in,2).lt.bfrag(2,j)) then - call bgrow(bstrand,nbstrand,in,2,bfrag(2,j)) - else - bstrand(nbstrand,6)=bstrand(nbstrand,6)- - & (bstrand(in,6)-bfrag(2,j)) - endif - endif - goto 11 - endif - enddo - endif - - - - ENDIF - enddo - - j=2 - do while (usedbfrag(j)) - j=j+1 - enddo - - nbstrand=nbstrand+1 - nbetasheet=nbetasheet+1 - bstrand(nbstrand,1)=bfrag(1,j) - bstrand(nbstrand,2)=bfrag(2,j) - bstrand(nbstrand,3)=nbetasheet - bstrand(nbstrand,5)=bfrag(1,j) - bstrand(nbstrand,6)=bfrag(2,j) - - bstrand(nbstrand,4)=nbstrand - do i=bfrag(1,j),bfrag(2,j) - betasheet(i)=nbetasheet - ibetasheet(i)=nbstrand - enddo -c - nbstrand=nbstrand+1 - bstrand(nbstrand,1)=bfrag(3,j) - bstrand(nbstrand,2)=bfrag(4,j) - bstrand(nbstrand,3)=nbetasheet - bstrand(nbstrand,5)=bfrag(3,j) - bstrand(nbstrand,6)=bfrag(4,j) - - if (bfrag(3,j).le.bfrag(4,j)) then - bstrand(nbstrand,4)=nbstrand - do i=bfrag(3,j),bfrag(4,j) - betasheet(i)=nbetasheet - ibetasheet(i)=nbstrand - enddo - else - bstrand(nbstrand,4)=-nbstrand - do i=bfrag(4,j),bfrag(3,j) - betasheet(i)=nbetasheet - ibetasheet(i)=nbstrand - enddo - endif - - iused_nbfrag=iused_nbfrag+1 - usedbfrag(j)=.true. - - - 11 continue - do jk=6,1,-1 - write (*,'(i4,a3,10i4)') jk,'A',(bstrand(i,jk),i=1,nbstrand) - enddo - - - enddo - - do i=1,nres - if (betasheet(i).ne.0) write(*,*) i,betasheet(i),ibetasheet(i) - enddo - write(*,*) - do j=6,1,-1 - write (*,'(i4,a3,10i4)') j,':',(bstrand(i,j),i=1,nbstrand) - enddo - -c------------------------ - nifb=0 - do i=1,nbstrand - do j=i+1,nbstrand - if(iabs(bstrand(i,5)-bstrand(j,5)).le.5 .or. - & iabs(bstrand(i,6)-bstrand(j,6)).le.5 ) then - nifb=nifb+1 - ifb(nifb,1)=bstrand(i,4) - ifb(nifb,2)=bstrand(j,4) - endif - enddo - enddo - - write(*,*) - do i=1,nifb - write (*,'(a3,20i4)') "ifb",i,ifb(i,1),ifb(i,2) - enddo - - do i=1,nbstrand - ifa(i)=bstrand(i,4) - enddo - write (*,'(a3,20i4)') "ifa",(ifa(i),i=1,nbstrand) - - nif=iabs(bstrand(1,6)-bstrand(1,5))+1 - do j=2,nbstrand - if (iabs(bstrand(j,6)-bstrand(j,5))+1.gt.nif) - & nif=iabs(bstrand(j,6)-bstrand(j,5))+1 - enddo - - write(*,*) nif - do i=1,nif - do j=1,nbstrand - if(j,i)=bstrand(j,6)+(i-1)*sign(1,bstrand(j,5)-bstrand(j,6)) - if (if(j,i).gt.0) then - if(betasheet(if(j,i)).eq.0 .or. - & ibetasheet(if(j,i)).ne.iabs(bstrand(j,4))) if(j,i)=0 - else - if(j,i)=0 - endif - enddo - write(*,'(a3,10i4)') 'if ',(if(j,i),j=1,nbstrand) - enddo - -c read (inp,*) (ifa(i),i=1,4) -c do i=1,nres -c read (inp,*,err=20,end=20) (if(j,i),j=1,4) -c enddo -c 20 nif=i-1 - stop -c------------------------ - - isa=4 - is=2*isa-1 - iconf=0 -cccccccccccccccccccccccccccccccccc - DO ig=1,is**isa-1 -cccccccccccccccccccccccccccccccccc - - ii=ig - do j=1,is - istrand(is-j+1)=int(ii/is**(is-j)) - ii=ii-istrand(is-j+1)*is**(is-j) - enddo - ltest=.true. - do k=1,isa - istrand(k)=istrand(k)+1 - if(istrand(k).gt.isa) istrand(k)=istrand(k)-2*isa-1 - enddo - do k=1,isa - do l=1,isa - if(istrand(k).eq.istrand(l).and.k.ne.l.or. - & istrand(k).eq.-istrand(l).and.k.ne.l) ltest=.false. - enddo - enddo - - lifb0=1 - do m=1,nifb - lifb(m)=0 - do k=1,isa-1 - if( - & ifb(m,1).eq.istrand(k).and.ifb(m,2).eq.istrand(k+1).or. - & ifb(m,2).eq.istrand(k).and.ifb(m,1).eq.istrand(k+1).or. - & -ifb(m,1).eq.istrand(k).and.-ifb(m,2).eq.istrand(k+1).or. - & -ifb(m,2).eq.istrand(k).and.-ifb(m,1).eq.istrand(k+1)) - & lifb(m)=1 - enddo - lifb0=lifb0*lifb(m) - enddo - - if (mod(isa,2).eq.0) then - do k=isa/2+1,isa - if (istrand(k).eq.1) ltest=.false. - enddo - else - do k=(isa+1)/2+1,isa - if (istrand(k).eq.1) ltest=.false. - enddo - endif - - IF (ltest.and.lifb0.eq.1) THEN - iconf=iconf+1 - - call var_to_geom(nvar,vorg) - - write (*,'(i5,i10,10i3)') iconf,ig,(istrand(k),k=1,isa) - write (iout,'(i5,i10,10i3)') iconf,ig,(istrand(k),k=1,isa) - write (linia,'(10i3)') (istrand(k),k=1,isa) - - do i=1,nres - do j=1,nres - ibc(i,j)=0 - enddo - enddo - - - do i=1,4 - if ( sign(1,istrand(i)).eq.sign(1,ifa(iabs(istrand(i)))) ) then - do j=1,nif - itmp(iabs(istrand(i)),j)=if(iabs(ifa(iabs(istrand(i)))),j) - enddo - else - do j=1,nif - itmp(iabs(istrand(i)),j)=if(iabs(ifa(iabs(istrand(i)))),nif-j+1) - enddo - endif - enddo - - do i=1,nif - write(*,*) (itmp(j,i),j=1,4) - enddo - - do i=1,nif -c ifa(1),ifa(2),ifa(3),ifa(4) -c if(1,i),if(2,i),if(3,i),if(4,i) - do k=1,isa-1 - ltest=.false. - do m=1,nifb - if( - & ifb(m,1).eq.istrand(k).and.ifb(m,2).eq.istrand(k+1).or. - & ifb(m,2).eq.istrand(k).and.ifb(m,1).eq.istrand(k+1).or. - & -ifb(m,1).eq.istrand(k).and.-ifb(m,2).eq.istrand(k+1).or. - & -ifb(m,2).eq.istrand(k).and.-ifb(m,1).eq.istrand(k+1)) - & then - ltest=.true. - goto 110 - endif - enddo - 110 continue - if (ltest) then - ibc(itmp(iabs(istrand(k)),i),itmp(iabs(istrand(k+1)),i))=-1 - else - ibc(itmp(iabs(istrand(k)),i),itmp(iabs(istrand(k+1)),i))=-2 - endif -c - if (k.lt.3) - & ibc(itmp(iabs(istrand(k)),i),itmp(iabs(istrand(k+2)),i))=-3 - if (k.lt.2) - & ibc(itmp(iabs(istrand(k)),i),itmp(iabs(istrand(k+3)),i))=-4 - enddo - enddo -c------------------------ - -c -c freeze sec.elements -c - do i=1,nres - mask(i)=1 - mask_phi(i)=1 - mask_theta(i)=1 - mask_side(i)=1 - enddo - - do j=1,nbfrag - do i=bfrag(1,j),bfrag(2,j) - mask(i)=0 - mask_phi(i)=0 - mask_theta(i)=0 - enddo - if (bfrag(3,j).le.bfrag(4,j)) then - do i=bfrag(3,j),bfrag(4,j) - mask(i)=0 - mask_phi(i)=0 - mask_theta(i)=0 - enddo - else - do i=bfrag(4,j),bfrag(3,j) - mask(i)=0 - mask_phi(i)=0 - mask_theta(i)=0 - enddo - endif - enddo - do j=1,nhfrag - do i=hfrag(1,j),hfrag(2,j) - mask(i)=0 - mask_phi(i)=0 - mask_theta(i)=0 - enddo - enddo - mask_r=.true. - -c------------------------ -c generate constrains -c - nhpb0=nhpb - call chainbuild - ind=0 - do i=1,nres-3 - do j=i+3,nres - ind=ind+1 - if ( ibc(i,j).eq.-1 .or. ibc(j,i).eq.-1) then - d0(ind)=DIST(i,j) - w(ind)=10.0 - nhpb=nhpb+1 - ihpb(nhpb)=i - jhpb(nhpb)=j - forcon(nhpb)=10.0 - dhpb(nhpb)=d0(ind) - else if ( ibc(i,j).eq.-2 .or. ibc(j,i).eq.-2) then - d0(ind)=5.0 - w(ind)=10.0 - nhpb=nhpb+1 - ihpb(nhpb)=i - jhpb(nhpb)=j - forcon(nhpb)=10.0 - dhpb(nhpb)=d0(ind) - else if ( ibc(i,j).eq.-3 .or. ibc(j,i).eq.-3) then - d0(ind)=11.0 - w(ind)=10.0 - nhpb=nhpb+1 - ihpb(nhpb)=i - jhpb(nhpb)=j - forcon(nhpb)=10.0 - dhpb(nhpb)=d0(ind) - else if ( ibc(i,j).eq.-4 .or. ibc(j,i).eq.-4) then - d0(ind)=16.0 - w(ind)=10.0 - nhpb=nhpb+1 - ihpb(nhpb)=i - jhpb(nhpb)=j - forcon(nhpb)=10.0 - dhpb(nhpb)=d0(ind) - else if ( ibc(i,j).gt.0 ) then - d0(ind)=DIST(i,ibc(i,j)) - w(ind)=10.0 - nhpb=nhpb+1 - ihpb(nhpb)=i - jhpb(nhpb)=j - forcon(nhpb)=10.0 - dhpb(nhpb)=d0(ind) - else if ( ibc(j,i).gt.0 ) then - d0(ind)=DIST(ibc(j,i),j) - w(ind)=10.0 - nhpb=nhpb+1 - ihpb(nhpb)=i - jhpb(nhpb)=j - forcon(nhpb)=10.0 - dhpb(nhpb)=d0(ind) - else - w(ind)=0.0 - endif - dd(ind)=d0(ind) - enddo - enddo - call hpb_partition -cd-------------------------- - - write(iout,'(i3,2i4,a3,2i4,f7.2)') (i,ibc(ihpb(i),jhpb(i)), - & ibc(jhpb(i),ihpb(i)),' --', - & ihpb(i),jhpb(i),dhpb(i),i=1,nhpb) - -cd nhpb=0 -cd goto 901 -c -c - call contact_cp_min(varia,ifun,iconf,linia,debug) - if (minim) then -#ifdef MPI - time0=MPI_WTIME() -#else - time0=tcpu() -#endif - call minimize(etot,varia,iretcode,nfun) - write(iout,*)'------------------------------------------------' - write(iout,*)'SUMSL return code is',iretcode,' eval ',nfun, - & '+ DIST eval',ifun - -#ifdef MPI - time1=MPI_WTIME() -#else - time1=tcpu() -#endif - write (iout,'(a,f6.2,f8.2,a)')' Time for full min.',time1-time0, - & nfun/(time1-time0),' eval/s' - - write (linia,'(a10,10i3)') 'full_min',(istrand(k),k=1,isa) - call var_to_geom(nvar,varia) - call chainbuild - call write_pdb(900+iconf,linia,etot) - endif - - call etotal(energy(0)) - etot=energy(0) - call enerprint(energy(0)) -cd call intout -cd call briefout(0,etot) -cd call secondary2(.true.) - - 901 CONTINUE -ctest return -cccccccccccccccccccccccccccccccccccc - ENDIF - ENDDO -cccccccccccccccccccccccccccccccccccc - - return - 10 write (iout,'(a)') 'Error reading test structure.' - return - end -c-------------------------------------------------------- - - subroutine test3 - implicit real*8 (a-h,o-z) - include 'DIMENSIONS' -#ifdef MPI - include 'mpif.h' -#endif - include 'COMMON.GEO' - include 'COMMON.CHAIN' - include 'COMMON.IOUNITS' - include 'COMMON.VAR' - include 'COMMON.CONTROL' - include 'COMMON.SBRIDGE' - include 'COMMON.FFIELD' - include 'COMMON.MINIM' -c - include 'COMMON.DISTFIT' - integer if(3,maxres),nif - integer ibc(maxres,maxres),istrand(20) - integer ibd(maxres),ifb(10,2),nifb,lifb(10),lifb0 - double precision time0,time1 - double precision energy(0:n_ene),ee - double precision varia(maxvar) -c - logical debug,ltest - character*50 linia -c - do i=1,nres - read (inp,*,err=20,end=20) if(1,i),if(2,i),if(3,i) - enddo - 20 nif=i-1 - write (*,'(a4,3i5)') ('if =',if(1,i),if(2,i),if(3,i), - & i=1,nif) - - -c------------------------ - call secondary2(debug) -c------------------------ - do i=1,nres - do j=1,nres - ibc(i,j)=0 - enddo - enddo - -c -c freeze sec.elements and store indexes for beta constrains -c - do i=1,nres - mask(i)=1 - mask_phi(i)=1 - mask_theta(i)=1 - mask_side(i)=1 - enddo - - do j=1,nbfrag - do i=bfrag(1,j),bfrag(2,j) - mask(i)=0 - mask_phi(i)=0 - mask_theta(i)=0 - enddo - if (bfrag(3,j).le.bfrag(4,j)) then - do i=bfrag(3,j),bfrag(4,j) - mask(i)=0 - mask_phi(i)=0 - mask_theta(i)=0 - ibc(bfrag(1,j)+i-bfrag(3,j),i)=-1 - enddo - else - do i=bfrag(4,j),bfrag(3,j) - mask(i)=0 - mask_phi(i)=0 - mask_theta(i)=0 - ibc(bfrag(2,j)-i+bfrag(4,j),i)=-1 - enddo - endif - enddo - do j=1,nhfrag - do i=hfrag(1,j),hfrag(2,j) - mask(i)=0 - mask_phi(i)=0 - mask_theta(i)=0 - enddo - enddo - mask_r=.true. - - -c ---------------- test -------------- - do i=1,nif - if (ibc(if(1,i),if(2,i)).eq.-1) then - ibc(if(1,i),if(2,i))=if(3,i) - ibc(if(1,i),if(3,i))=if(2,i) - else if (ibc(if(2,i),if(1,i)).eq.-1) then - ibc(if(2,i),if(1,i))=0 - ibc(if(1,i),if(2,i))=if(3,i) - ibc(if(1,i),if(3,i))=if(2,i) - else - ibc(if(1,i),if(2,i))=if(3,i) - ibc(if(1,i),if(3,i))=if(2,i) - endif - enddo - - do i=1,nres - do j=1,nres - if (ibc(i,j).ne.0) write(*,'(3i5)') i,j,ibc(i,j) - enddo - enddo -c------------------------ - call chainbuild - ind=0 - do i=1,nres-3 - do j=i+3,nres - ind=ind+1 - if ( ibc(i,j).eq.-1 ) then - d0(ind)=DIST(i,j) - w(ind)=10.0 - nhpb=nhpb+1 - ihpb(nhpb)=i - jhpb(nhpb)=j - forcon(nhpb)=10.0 - dhpb(nhpb)=d0(ind) - else if ( ibc(i,j).gt.0 ) then - d0(ind)=DIST(i,ibc(i,j)) - w(ind)=10.0 - nhpb=nhpb+1 - ihpb(nhpb)=i - jhpb(nhpb)=j - forcon(nhpb)=10.0 - dhpb(nhpb)=d0(ind) - else if ( ibc(j,i).gt.0 ) then - d0(ind)=DIST(ibc(j,i),j) - w(ind)=10.0 - nhpb=nhpb+1 - ihpb(nhpb)=i - jhpb(nhpb)=j - forcon(nhpb)=10.0 - dhpb(nhpb)=d0(ind) - else - w(ind)=0.0 - endif - enddo - enddo - call hpb_partition - -cd-------------------------- - write(*,'(i3,2i4,a3,2i4,f7.2)') (i,ibc(ihpb(i),jhpb(i)), - & ibc(jhpb(i),ihpb(i)),' --', - & ihpb(i),jhpb(i),dhpb(i),i=1,nhpb) - - - linia='dist' - debug=.true. - in_pdb=7 -c - call contact_cp_min(varia,ieval,in_pdb,linia,debug) - if (minim) then -#ifdef MPI - time0=MPI_WTIME() -#else - time0=tcpu() -#endif - call minimize(etot,varia,iretcode,nfun) - write(iout,*)'------------------------------------------------' - write(iout,*)'SUMSL return code is',iretcode,' eval ',nfun, - & '+ DIST eval',ieval - -#ifdef MPI - time1=MPI_WTIME() -#else - time1=tcpu() -#endif - write (iout,'(a,f6.2,f8.2,a)')' Time for full min.',time1-time0, - & nfun/(time1-time0),' eval/s' - - - call var_to_geom(nvar,varia) - call chainbuild - call write_pdb(999,'full min',etot) - endif - - call etotal(energy(0)) - etot=energy(0) - call enerprint(energy(0)) - call intout - call briefout(0,etot) - call secondary2(.true.) - - return - 10 write (iout,'(a)') 'Error reading test structure.' - return - end - - - - - subroutine test__ - implicit real*8 (a-h,o-z) - include 'DIMENSIONS' -#ifdef MPI - include 'mpif.h' -#endif - include 'COMMON.GEO' - include 'COMMON.CHAIN' - include 'COMMON.IOUNITS' - include 'COMMON.VAR' - include 'COMMON.CONTROL' - include 'COMMON.SBRIDGE' - include 'COMMON.FFIELD' - include 'COMMON.MINIM' -c - include 'COMMON.DISTFIT' - integer if(2,2),ind - integer iff(maxres) - double precision time0,time1 - double precision energy(0:n_ene),ee - double precision theta2(maxres),phi2(maxres),alph2(maxres), - & omeg2(maxres), - & theta1(maxres),phi1(maxres),alph1(maxres), - & omeg1(maxres) - double precision varia(maxvar),varia2(maxvar) -c - - - read (inp,*,err=10,end=10) if(1,1),if(1,2),if(2,1),if(2,2) - write (iout,'(a4,4i5)') 'if =',if(1,1),if(1,2),if(2,1),if(2,2) - read (inp,*,err=10,end=10) (theta2(i),i=3,nres) - read (inp,*,err=10,end=10) (phi2(i),i=4,nres) - read (inp,*,err=10,end=10) (alph2(i),i=2,nres-1) - read (inp,*,err=10,end=10) (omeg2(i),i=2,nres-1) - do i=1,nres - theta2(i)=deg2rad*theta2(i) - phi2(i)=deg2rad*phi2(i) - alph2(i)=deg2rad*alph2(i) - omeg2(i)=deg2rad*omeg2(i) - enddo - do i=1,nres - theta1(i)=theta(i) - phi1(i)=phi(i) - alph1(i)=alph(i) - omeg1(i)=omeg(i) - enddo - - do i=1,nres - mask(i)=1 - enddo - - -c------------------------ - do i=1,nres - iff(i)=0 - enddo - do j=1,2 - do i=if(j,1),if(j,2) - iff(i)=1 - enddo - enddo - - call chainbuild - call geom_to_var(nvar,varia) - call write_pdb(1,'first structure',0d0) - - call secondary(.true.) - - call secondary2(.true.) - - do j=1,nbfrag - if ( (bfrag(3,j).lt.bfrag(4,j) .or. - & bfrag(4,j)-bfrag(2,j).gt.4) .and. - & bfrag(2,j)-bfrag(1,j).gt.3 ) then - nn=nn+1 - - if (bfrag(3,j).lt.bfrag(4,j)) then - write(iout,'(a6,i3,a1,i3,a1,i3,a1,i3)') - & "select",bfrag(1,j)-1,"-",bfrag(2,j)-1 - & ,",",bfrag(3,j)-1,"-",bfrag(4,j)-1 - else - write(iout,'(a6,i3,a1,i3,a1,i3,a1,i3)') - & "select",bfrag(1,j)-1,"-",bfrag(2,j)-1 - & ,",",bfrag(4,j)-1,"-",bfrag(3,j)-1 - endif - endif - enddo - - do i=1,nres - theta(i)=theta2(i) - phi(i)=phi2(i) - alph(i)=alph2(i) - omeg(i)=omeg2(i) - enddo - - call chainbuild - call geom_to_var(nvar,varia2) - call write_pdb(2,'second structure',0d0) - - - -c------------------------------------------------------- - - ifun=-1 - call contact_cp(varia,varia2,iff,ifun,7) - if (minim) then -#ifdef MPI - time0=MPI_WTIME() -#else - time0=tcpu() -#endif - call minimize(etot,varia,iretcode,nfun) - write(iout,*)'------------------------------------------------' - write(iout,*)'SUMSL return code is',iretcode,' eval ',nfun, - & '+ DIST eval',ifun - -#ifdef MPI - time1=MPI_WTIME() -#else - time1=tcpu() -#endif - write (iout,'(a,f6.2,f8.2,a)')' Time for full min.',time1-time0, - & nfun/(time1-time0),' eval/s' - - - call var_to_geom(nvar,varia) - call chainbuild - call write_pdb(999,'full min',etot) - endif - - call etotal(energy(0)) - etot=energy(0) - call enerprint(energy(0)) - call intout - call briefout(0,etot) - - return - 10 write (iout,'(a)') 'Error reading test structure.' - return - end - -c------------------------------------------------- -c------------------------------------------------- - - subroutine secondary(lprint) - implicit real*8 (a-h,o-z) - include 'DIMENSIONS' - include 'COMMON.CHAIN' - include 'COMMON.IOUNITS' - include 'COMMON.DISTFIT' - - integer ncont,icont(2,maxres*maxres/2),isec(maxres,3) - logical lprint,not_done - real dcont(maxres*maxres/2),d - real rcomp /7.0/ - real rbeta /5.2/ - real ralfa /5.2/ - real r310 /6.6/ - double precision xpi(3),xpj(3) - - - - call chainbuild -cd call write_pdb(99,'sec structure',0d0) - ncont=0 - nbfrag=0 - nhfrag=0 - do i=1,nres - isec(i,1)=0 - isec(i,2)=0 - isec(i,3)=0 - enddo - - do i=2,nres-3 - do k=1,3 - xpi(k)=0.5d0*(c(k,i-1)+c(k,i)) - enddo - do j=i+2,nres - do k=1,3 - xpj(k)=0.5d0*(c(k,j-1)+c(k,j)) - enddo -cd d = (c(1,i)-c(1,j))*(c(1,i)-c(1,j)) + -cd & (c(2,i)-c(2,j))*(c(2,i)-c(2,j)) + -cd & (c(3,i)-c(3,j))*(c(3,i)-c(3,j)) -cd print *,'CA',i,j,d - d = (xpi(1)-xpj(1))*(xpi(1)-xpj(1)) + - & (xpi(2)-xpj(2))*(xpi(2)-xpj(2)) + - & (xpi(3)-xpj(3))*(xpi(3)-xpj(3)) - if ( d.lt.rcomp*rcomp) then - ncont=ncont+1 - icont(1,ncont)=i - icont(2,ncont)=j - dcont(ncont)=sqrt(d) - endif - enddo - enddo - if (lprint) then - write (iout,*) - write (iout,'(a)') '#PP contact map distances:' - do i=1,ncont - write (iout,'(3i4,f10.5)') - & i,icont(1,i),icont(2,i),dcont(i) - enddo - endif - -c finding parallel beta -cd write (iout,*) '------- looking for parallel beta -----------' - nbeta=0 - nstrand=0 - do i=1,ncont - i1=icont(1,i) - j1=icont(2,i) - if(dcont(i).le.rbeta .and. j1-i1.gt.4 .and. - & isec(i1,1).le.1.and.isec(j1,1).le.1.and. - & (isec(i1,2).ne.isec(j1,2).or.isec(i1,2)*isec(j1,2).eq.0).and. - & (isec(i1,3).ne.isec(j1,3).or.isec(i1,3)*isec(j1,3).eq.0).and. - & (isec(i1,2).ne.isec(j1,3).or.isec(i1,2)*isec(j1,3).eq.0).and. - & (isec(i1,3).ne.isec(j1,2).or.isec(i1,3)*isec(j1,2).eq.0) - & ) then - ii1=i1 - jj1=j1 -cd write (iout,*) i1,j1,dcont(i) - not_done=.true. - do while (not_done) - i1=i1+1 - j1=j1+1 - do j=1,ncont - if (i1.eq.icont(1,j) .and. j1.eq.icont(2,j) - & .and. dcont(j).le.rbeta .and. - & isec(i1,1).le.1.and.isec(j1,1).le.1.and. - & (isec(i1,2).ne.isec(j1,2).or.isec(i1,2)*isec(j1,2).eq.0).and. - & (isec(i1,3).ne.isec(j1,3).or.isec(i1,3)*isec(j1,3).eq.0).and. - & (isec(i1,2).ne.isec(j1,3).or.isec(i1,2)*isec(j1,3).eq.0).and. - & (isec(i1,3).ne.isec(j1,2).or.isec(i1,3)*isec(j1,2).eq.0) - & ) goto 5 - enddo - not_done=.false. - 5 continue -cd write (iout,*) i1,j1,dcont(j),not_done - enddo - j1=j1-1 - i1=i1-1 - if (i1-ii1.gt.1) then - ii1=max0(ii1-1,1) - jj1=max0(jj1-1,1) - nbeta=nbeta+1 - if(lprint)write(iout,*)'parallel beta',nbeta,ii1,i1,jj1,j1 - - nbfrag=nbfrag+1 - bfrag(1,nbfrag)=ii1 - bfrag(2,nbfrag)=i1 - bfrag(3,nbfrag)=jj1 - bfrag(4,nbfrag)=j1 - - do ij=ii1,i1 - isec(ij,1)=isec(ij,1)+1 - isec(ij,1+isec(ij,1))=nbeta - enddo - do ij=jj1,j1 - isec(ij,1)=isec(ij,1)+1 - isec(ij,1+isec(ij,1))=nbeta - enddo - - if(lprint) then - nstrand=nstrand+1 - if (nbeta.le.9) then - write(12,'(a18,i1,a9,i3,a2,i3,a1)') - & "DefPropRes 'strand",nstrand, - & "' 'num = ",ii1-1,"..",i1-1,"'" - else - write(12,'(a18,i2,a9,i3,a2,i3,a1)') - & "DefPropRes 'strand",nstrand, - & "' 'num = ",ii1-1,"..",i1-1,"'" - endif - nstrand=nstrand+1 - if (nbeta.le.9) then - write(12,'(a18,i1,a9,i3,a2,i3,a1)') - & "DefPropRes 'strand",nstrand, - & "' 'num = ",jj1-1,"..",j1-1,"'" - else - write(12,'(a18,i2,a9,i3,a2,i3,a1)') - & "DefPropRes 'strand",nstrand, - & "' 'num = ",jj1-1,"..",j1-1,"'" - endif - write(12,'(a8,4i4)') - & "SetNeigh",ii1-1,i1-1,jj1-1,j1-1 - endif - endif - endif - enddo - -c finding antiparallel beta -cd write (iout,*) '--------- looking for antiparallel beta ---------' - - do i=1,ncont - i1=icont(1,i) - j1=icont(2,i) - if (dcont(i).le.rbeta.and. - & isec(i1,1).le.1.and.isec(j1,1).le.1.and. - & (isec(i1,2).ne.isec(j1,2).or.isec(i1,2)*isec(j1,2).eq.0).and. - & (isec(i1,3).ne.isec(j1,3).or.isec(i1,3)*isec(j1,3).eq.0).and. - & (isec(i1,2).ne.isec(j1,3).or.isec(i1,2)*isec(j1,3).eq.0).and. - & (isec(i1,3).ne.isec(j1,2).or.isec(i1,3)*isec(j1,2).eq.0) - & ) then - ii1=i1 - jj1=j1 -cd write (iout,*) i1,j1,dcont(i) - - not_done=.true. - do while (not_done) - i1=i1+1 - j1=j1-1 - do j=1,ncont - if (i1.eq.icont(1,j).and.j1.eq.icont(2,j) .and. - & isec(i1,1).le.1.and.isec(j1,1).le.1.and. - & (isec(i1,2).ne.isec(j1,2).or.isec(i1,2)*isec(j1,2).eq.0).and. - & (isec(i1,3).ne.isec(j1,3).or.isec(i1,3)*isec(j1,3).eq.0).and. - & (isec(i1,2).ne.isec(j1,3).or.isec(i1,2)*isec(j1,3).eq.0).and. - & (isec(i1,3).ne.isec(j1,2).or.isec(i1,3)*isec(j1,2).eq.0) - & .and. dcont(j).le.rbeta ) goto 6 - enddo - not_done=.false. - 6 continue -cd write (iout,*) i1,j1,dcont(j),not_done - enddo - i1=i1-1 - j1=j1+1 - if (i1-ii1.gt.1) then - if(lprint)write (iout,*)'antiparallel beta', - & nbeta,ii1-1,i1,jj1,j1-1 - - nbfrag=nbfrag+1 - bfrag(1,nbfrag)=max0(ii1-1,1) - bfrag(2,nbfrag)=i1 - bfrag(3,nbfrag)=jj1 - bfrag(4,nbfrag)=max0(j1-1,1) - - nbeta=nbeta+1 - iii1=max0(ii1-1,1) - do ij=iii1,i1 - isec(ij,1)=isec(ij,1)+1 - isec(ij,1+isec(ij,1))=nbeta - enddo - jjj1=max0(j1-1,1) - do ij=jjj1,jj1 - isec(ij,1)=isec(ij,1)+1 - isec(ij,1+isec(ij,1))=nbeta - enddo - - - if (lprint) then - nstrand=nstrand+1 - if (nstrand.le.9) then - write(12,'(a18,i1,a9,i3,a2,i3,a1)') - & "DefPropRes 'strand",nstrand, - & "' 'num = ",ii1-2,"..",i1-1,"'" - else - write(12,'(a18,i2,a9,i3,a2,i3,a1)') - & "DefPropRes 'strand",nstrand, - & "' 'num = ",ii1-2,"..",i1-1,"'" - endif - nstrand=nstrand+1 - if (nstrand.le.9) then - write(12,'(a18,i1,a9,i3,a2,i3,a1)') - & "DefPropRes 'strand",nstrand, - & "' 'num = ",j1-2,"..",jj1-1,"'" - else - write(12,'(a18,i2,a9,i3,a2,i3,a1)') - & "DefPropRes 'strand",nstrand, - & "' 'num = ",j1-2,"..",jj1-1,"'" - endif - write(12,'(a8,4i4)') - & "SetNeigh",ii1-2,i1-1,jj1-1,j1-2 - endif - endif - endif - enddo - - if (nstrand.gt.0.and.lprint) then - write(12,'(a27,$)') "DefPropRes 'sheet' 'strand1" - do i=2,nstrand - if (i.le.9) then - write(12,'(a9,i1,$)') " | strand",i - else - write(12,'(a9,i2,$)') " | strand",i - endif - enddo - write(12,'(a1)') "'" - endif - - -c finding alpha or 310 helix - - nhelix=0 - do i=1,ncont - i1=icont(1,i) - j1=icont(2,i) - if (j1.eq.i1+3.and.dcont(i).le.r310 - & .or.j1.eq.i1+4.and.dcont(i).le.ralfa ) then -cd if (j1.eq.i1+3) write (iout,*) "found 1-4 ",i1,j1,dcont(i) -cd if (j1.eq.i1+4) write (iout,*) "found 1-5 ",i1,j1,dcont(i) - ii1=i1 - jj1=j1 - if (isec(ii1,1).eq.0) then - not_done=.true. - else - not_done=.false. - endif - do while (not_done) - i1=i1+1 - j1=j1+1 - do j=1,ncont - if (i1.eq.icont(1,j) .and. j1.eq.icont(2,j)) goto 10 - enddo - not_done=.false. - 10 continue -cd write (iout,*) i1,j1,not_done - enddo - j1=j1-1 - if (j1-ii1.gt.4) then - nhelix=nhelix+1 -cd write (iout,*)'helix',nhelix,ii1,j1 - - nhfrag=nhfrag+1 - hfrag(1,nhfrag)=ii1 - hfrag(2,nhfrag)=max0(j1-1,1) - - do ij=ii1,j1 - isec(ij,1)=-1 - enddo - if (lprint) then - write (iout,'(a6,i3,2i4)') "Helix",nhelix,ii1-1,j1-2 - if (nhelix.le.9) then - write(12,'(a17,i1,a9,i3,a2,i3,a1)') - & "DefPropRes 'helix",nhelix, - & "' 'num = ",ii1-1,"..",j1-2,"'" - else - write(12,'(a17,i2,a9,i3,a2,i3,a1)') - & "DefPropRes 'helix",nhelix, - & "' 'num = ",ii1-1,"..",j1-2,"'" - endif - endif - endif - endif - enddo - - if (nhelix.gt.0.and.lprint) then - write(12,'(a26,$)') "DefPropRes 'helix' 'helix1" - do i=2,nhelix - if (nhelix.le.9) then - write(12,'(a8,i1,$)') " | helix",i - else - write(12,'(a8,i2,$)') " | helix",i - endif - enddo - write(12,'(a1)') "'" - endif - - if (lprint) then - write(12,'(a37)') "DefPropRes 'coil' '! (helix | sheet)'" - write(12,'(a20)') "XMacStand ribbon.mac" - endif - - - return - end -c---------------------------------------------------------------------------- - - subroutine write_pdb(npdb,titelloc,ee) - implicit real*8 (a-h,o-z) - include 'DIMENSIONS' - include 'COMMON.IOUNITS' - character*50 titelloc1 - character*(*) titelloc - character*3 zahl - character*5 liczba5 - double precision ee - integer npdb,ilen - external ilen - - titelloc1=titelloc - lenpre=ilen(prefix) - if (npdb.lt.1000) then - call numstr(npdb,zahl) - open(ipdb,file=prefix(:lenpre)//'@@'//zahl//'.pdb') - else - if (npdb.lt.10000) then - write(liczba5,'(i1,i4)') 0,npdb - else - write(liczba5,'(i5)') npdb - endif - open(ipdb,file=prefix(:lenpre)//'@@'//liczba5//'.pdb') - endif - call pdbout(ee,titelloc1,ipdb) - close(ipdb) - return - end - -c----------------------------------------------------------- - subroutine contact_cp2(var,var2,iff,ieval,in_pdb) - implicit real*8 (a-h,o-z) - include 'DIMENSIONS' -#ifdef MPI - include 'mpif.h' -#endif - include 'COMMON.SBRIDGE' - include 'COMMON.FFIELD' - include 'COMMON.IOUNITS' - include 'COMMON.DISTFIT' - include 'COMMON.VAR' - include 'COMMON.CHAIN' - include 'COMMON.MINIM' - - character*50 linia - integer nf,ij(4) - double precision var(maxvar),var2(maxvar) - double precision time0,time1 - integer iff(maxres),ieval - double precision theta1(maxres),phi1(maxres),alph1(maxres), - & omeg1(maxres) - - - call var_to_geom(nvar,var) - call chainbuild - nhpb0=nhpb - ind=0 - do i=1,nres-3 - do j=i+3,nres - ind=ind+1 - if ( iff(i).eq.1.and.iff(j).eq.1 ) then - d0(ind)=DIST(i,j) - w(ind)=10.0 - nhpb=nhpb+1 - ihpb(nhpb)=i - jhpb(nhpb)=j - forcon(nhpb)=10.0 - dhpb(nhpb)=d0(ind) - else - w(ind)=0.0 - endif - enddo - enddo - call hpb_partition - - do i=1,nres - theta1(i)=theta(i) - phi1(i)=phi(i) - alph1(i)=alph(i) - omeg1(i)=omeg(i) - enddo - - call var_to_geom(nvar,var2) - - do i=1,nres - if ( iff(i).eq.1 ) then - theta(i)=theta1(i) - phi(i)=phi1(i) - alph(i)=alph1(i) - omeg(i)=omeg1(i) - endif - enddo - - call chainbuild - - NX=NRES-3 - NY=((NRES-4)*(NRES-5))/2 - call distfit(.true.,200) - - - ipot0=ipot - maxmin0=maxmin - maxfun0=maxfun - wstrain0=wstrain - - ipot=6 - maxmin=2000 - maxfun=5000 - call geom_to_var(nvar,var) - call minimize(etot,var,iretcode,nfun) - write(iout,*)'SUMSL return code is',iretcode,' eval SOFT',nfun - - call var_to_geom(nvar,var) - call chainbuild - - - iwsk=0 - nf=0 - if (iff(1).eq.1) then - iwsk=1 - nf=nf+1 - ij(nf)=0 - endif - do i=2,nres - if ( iwsk.eq.0.and.iff(i-1).eq.0.and.iff(i).eq.1 ) then - iwsk=1 - nf=nf+1 - ij(nf)=i - endif - if ( iwsk.eq.1.and.iff(i-1).eq.1.and.iff(i).eq.0 ) then - iwsk=0 - nf=nf+1 - ij(nf)=i-1 - endif - enddo - if (iff(nres).eq.1) then - nf=nf+1 - ij(nf)=nres - endif - - -cd write(linia,'(a6,i3,a1,i3,a1,i3,a1,i3)') -cd & "select",ij(1),"-",ij(2), -cd & ",",ij(3),"-",ij(4) -cd call write_pdb(in_pdb,linia,etot) - - - ipot=ipot0 - maxmin=maxmin0 - maxfun=maxfun0 - call minimize(etot,var,iretcode,nfun) - ieval=nfun - - nhpb= nhpb0 - link_start=1 - link_end=nhpb - wstrain=wstrain0 - - return - end -c----------------------------------------------------------- - subroutine contact_cp(var,var2,iff,ieval,in_pdb) - implicit real*8 (a-h,o-z) - include 'DIMENSIONS' - include 'COMMON.SBRIDGE' - include 'COMMON.FFIELD' - include 'COMMON.IOUNITS' - include 'COMMON.DISTFIT' - include 'COMMON.VAR' - include 'COMMON.CHAIN' - include 'COMMON.MINIM' - - character*50 linia - integer nf,ij(4) - double precision energy(0:n_ene) - double precision var(maxvar),var2(maxvar) - double precision time0,time1 - integer iff(maxres),ieval - double precision theta1(maxres),phi1(maxres),alph1(maxres), - & omeg1(maxres) - logical debug - - debug=.false. -c debug=.true. - if (ieval.eq.-1) debug=.true. - - -c -c store selected dist. constrains from 1st structure -c -#ifdef OSF -c Intercept NaNs in the coordinates -c write(iout,*) (var(i),i=1,nvar) - x_sum=0.D0 - do i=1,nvar - x_sum=x_sum+var(i) - enddo - if (x_sum.ne.x_sum) then - write(iout,*)" *** contact_cp : Found NaN in coordinates" - call flush(iout) - print *," *** contact_cp : Found NaN in coordinates" - return - endif -#endif - - - call var_to_geom(nvar,var) - call chainbuild - nhpb0=nhpb - ind=0 - do i=1,nres-3 - do j=i+3,nres - ind=ind+1 - if ( iff(i).eq.1.and.iff(j).eq.1 ) then - d0(ind)=DIST(i,j) - w(ind)=10.0 - nhpb=nhpb+1 - ihpb(nhpb)=i - jhpb(nhpb)=j - forcon(nhpb)=10.0 - dhpb(nhpb)=d0(ind) - else - w(ind)=0.0 - endif - enddo - enddo - call hpb_partition - - do i=1,nres - theta1(i)=theta(i) - phi1(i)=phi(i) - alph1(i)=alph(i) - omeg1(i)=omeg(i) - enddo - -c -c freeze sec.elements from 2nd structure -c - do i=1,nres - mask_phi(i)=1 - mask_theta(i)=1 - mask_side(i)=1 - enddo - - call var_to_geom(nvar,var2) - call secondary2(debug) - do j=1,nbfrag - do i=bfrag(1,j),bfrag(2,j) - mask(i)=0 - mask_phi(i)=0 - mask_theta(i)=0 - enddo - if (bfrag(3,j).le.bfrag(4,j)) then - do i=bfrag(3,j),bfrag(4,j) - mask(i)=0 - mask_phi(i)=0 - mask_theta(i)=0 - enddo - else - do i=bfrag(4,j),bfrag(3,j) - mask(i)=0 - mask_phi(i)=0 - mask_theta(i)=0 - enddo - endif - enddo - do j=1,nhfrag - do i=hfrag(1,j),hfrag(2,j) - mask(i)=0 - mask_phi(i)=0 - mask_theta(i)=0 - enddo - enddo - mask_r=.true. - -c -c copy selected res from 1st to 2nd structure -c - - do i=1,nres - if ( iff(i).eq.1 ) then - theta(i)=theta1(i) - phi(i)=phi1(i) - alph(i)=alph1(i) - omeg(i)=omeg1(i) - endif - enddo - - if(debug) then -c -c prepare description in linia variable -c - iwsk=0 - nf=0 - if (iff(1).eq.1) then - iwsk=1 - nf=nf+1 - ij(nf)=1 - endif - do i=2,nres - if ( iwsk.eq.0.and.iff(i-1).eq.0.and.iff(i).eq.1 ) then - iwsk=1 - nf=nf+1 - ij(nf)=i - endif - if ( iwsk.eq.1.and.iff(i-1).eq.1.and.iff(i).eq.0 ) then - iwsk=0 - nf=nf+1 - ij(nf)=i-1 - endif - enddo - if (iff(nres).eq.1) then - nf=nf+1 - ij(nf)=nres - endif - - write(linia,'(a6,i3,a1,i3,a1,i3,a1,i3)') - & "SELECT",ij(1)-1,"-",ij(2)-1, - & ",",ij(3)-1,"-",ij(4)-1 - - endif -c -c run optimization -c - call contact_cp_min(var,ieval,in_pdb,linia,debug) - - return - end - - subroutine contact_cp_min(var,ieval,in_pdb,linia,debug) -c -c input : theta,phi,alph,omeg,in_pdb,linia,debug -c output : var,ieval -c - implicit real*8 (a-h,o-z) - include 'DIMENSIONS' -#ifdef MPI - include 'mpif.h' -#endif - include 'COMMON.SBRIDGE' - include 'COMMON.FFIELD' - include 'COMMON.IOUNITS' - include 'COMMON.DISTFIT' - include 'COMMON.VAR' - include 'COMMON.CHAIN' - include 'COMMON.MINIM' - - character*50 linia - integer nf,ij(4) - double precision energy(0:n_ene) - double precision var(maxvar) - double precision time0,time1 - integer ieval,info(3) - logical debug,fail,check_var,reduce,change - - write(iout,'(a20,i6,a20)') - & '------------------',in_pdb,'-------------------' - - if (debug) then - call chainbuild - call write_pdb(1000+in_pdb,'combined structure',0d0) -#ifdef MPI - time0=MPI_WTIME() -#else - time0=tcpu() -#endif - endif - -c -c run optimization of distances -c -c uses d0(),w() and mask() for frozen 2D -c -ctest--------------------------------------------- -ctest NX=NRES-3 -ctest NY=((NRES-4)*(NRES-5))/2 -ctest call distfit(debug,5000) - - do i=1,nres - mask_side(i)=0 - enddo - - ipot01=ipot - maxmin01=maxmin - maxfun01=maxfun -c wstrain01=wstrain - wsc01=wsc - wscp01=wscp - welec01=welec - wvdwpp01=wvdwpp -c wang01=wang - wscloc01=wscloc - wtor01=wtor - wtor_d01=wtor_d - - ipot=6 - maxmin=2000 - maxfun=4000 -c wstrain=1.0 - wsc=0.0 - wscp=0.0 - welec=0.0 - wvdwpp=0.0 -c wang=0.0 - wscloc=0.0 - wtor=0.0 - wtor_d=0.0 - - call geom_to_var(nvar,var) -cde change=reduce(var) - if (check_var(var,info)) then - write(iout,*) 'cp_min error in input' - print *,'cp_min error in input' - return - endif - -cd call etotal(energy(0)) -cd call enerprint(energy(0)) -cd call check_eint - -#ifdef MPI - time0=MPI_WTIME() -#else - time0=tcpu() -#endif -cdtest call minimize(etot,var,iretcode,nfun) -cdtest write(iout,*)'SUMSL return code is',iretcode,' eval SDIST',nfun -#ifdef MPI - time1=MPI_WTIME() -#else - time1=tcpu() -#endif - -cd call etotal(energy(0)) -cd call enerprint(energy(0)) -cd call check_eint - - do i=1,nres - mask_side(i)=1 - enddo - - ipot=ipot01 - maxmin=maxmin01 - maxfun=maxfun01 -c wstrain=wstrain01 - wsc=wsc01 - wscp=wscp01 - welec=welec01 - wvdwpp=wvdwpp01 -c wang=wang01 - wscloc=wscloc01 - wtor=wtor01 - wtor_d=wtor_d01 -ctest-------------------------------------------------- - - if(debug) then -#ifdef MPI - time1=MPI_WTIME() -#else - time1=tcpu() -#endif - write (iout,'(a,f6.2,a)')' Time for distfit ',time1-time0,' sec' - call write_pdb(2000+in_pdb,'distfit structure',0d0) - endif - - - ipot0=ipot - maxmin0=maxmin - maxfun0=maxfun - wstrain0=wstrain -c -c run soft pot. optimization -c with constrains: -c nhpb,ihpb(),jhpb(),forcon(),dhpb() and hpb_partition -c and frozen 2D: -c mask_phi(),mask_theta(),mask_side(),mask_r -c - ipot=6 - maxmin=2000 - maxfun=4000 - -cde change=reduce(var) -cde if (check_var(var,info)) write(iout,*) 'error before soft' -#ifdef MPI - time0=MPI_WTIME() -#else - time0=tcpu() -#endif - call minimize(etot,var,iretcode,nfun) - - write(iout,*)'SUMSL return code is',iretcode,' eval SOFT',nfun -#ifdef MPI - time1=MPI_WTIME() -#else - time1=tcpu() -#endif - write (iout,'(a,f6.2,f8.2,a)')' Time for soft min.',time1-time0, - & nfun/(time1-time0),' SOFT eval/s' - if (debug) then - call var_to_geom(nvar,var) - call chainbuild - call write_pdb(3000+in_pdb,'soft structure',etot) - endif -c -c run full UNRES optimization with constrains and frozen 2D -c the same variables as soft pot. optimizatio -c - ipot=ipot0 - maxmin=maxmin0 - maxfun=maxfun0 -c -c check overlaps before calling full UNRES minim -c - call var_to_geom(nvar,var) - call chainbuild - call etotal(energy(0)) -#ifdef OSF - write(iout,*) 'N7 ',energy(0) - if (energy(0).ne.energy(0)) then - write(iout,*) 'N7 error - gives NaN',energy(0) - endif -#endif - ieval=1 - if (energy(1).eq.1.0d20) then - write (iout,'(a,1pe14.5)')'#N7_OVERLAP evdw=1d20',energy(1) - call overlap_sc(fail) - if(.not.fail) then - call etotal(energy(0)) - ieval=ieval+1 - write (iout,'(a,1pe14.5)')'#N7_OVERLAP evdw after',energy(1) - else - mask_r=.false. - nhpb= nhpb0 - link_start=1 - link_end=nhpb - wstrain=wstrain0 - return - endif - endif - call flush(iout) -c -cdte time0=MPI_WTIME() -cde change=reduce(var) -cde if (check_var(var,info)) then -cde write(iout,*) 'error before mask dist' -cde call var_to_geom(nvar,var) -cde call chainbuild -cde call write_pdb(10000+in_pdb,'before mask dist',etot) -cde endif -cdte call minimize(etot,var,iretcode,nfun) -cdte write(iout,*)'SUMSL MASK DIST return code is',iretcode, -cdte & ' eval ',nfun -cdte ieval=ieval+nfun -cdte -cdte time1=MPI_WTIME() -cdte write (iout,'(a,f6.2,f8.2,a)') -cdte & ' Time for mask dist min.',time1-time0, -cdte & nfun/(time1-time0),' eval/s' -cdte call flush(iout) - if (debug) then - call var_to_geom(nvar,var) - call chainbuild - call write_pdb(4000+in_pdb,'mask dist',etot) - endif -c -c switch off freezing of 2D and -c run full UNRES optimization with constrains -c - mask_r=.false. -#ifdef MPI - time0=MPI_WTIME() -#else - time0=tcpu() -#endif -cde change=reduce(var) -cde if (check_var(var,info)) then -cde write(iout,*) 'error before dist' -cde call var_to_geom(nvar,var) -cde call chainbuild -cde call write_pdb(11000+in_pdb,'before dist',etot) -cde endif - - call minimize(etot,var,iretcode,nfun) - -cde change=reduce(var) -cde if (check_var(var,info)) then -cde write(iout,*) 'error after dist',ico -cde call var_to_geom(nvar,var) -cde call chainbuild -cde call write_pdb(12000+in_pdb+ico*1000,'after dist',etot) -cde endif - write(iout,*)'SUMSL DIST return code is',iretcode,' eval ',nfun - ieval=ieval+nfun - -#ifdef MPI - time1=MPI_WTIME() -#else - time1=tcpu() -#endif - write (iout,'(a,f6.2,f8.2,a)')' Time for dist min.',time1-time0, - & nfun/(time1-time0),' eval/s' -cde call etotal(energy(0)) -cde write(iout,*) 'N7 after dist',energy(0) - call flush(iout) - - if (debug) then - call var_to_geom(nvar,var) - call chainbuild - call write_pdb(in_pdb,linia,etot) - endif -c -c reset constrains -c - nhpb= nhpb0 - link_start=1 - link_end=nhpb - wstrain=wstrain0 - - return - end -c-------------------------------------------------------- - subroutine softreg - implicit real*8 (a-h,o-z) - include 'DIMENSIONS' -#ifdef MPI - include 'mpif.h' -#endif - include 'COMMON.GEO' - include 'COMMON.CHAIN' - include 'COMMON.IOUNITS' - include 'COMMON.VAR' - include 'COMMON.CONTROL' - include 'COMMON.SBRIDGE' - include 'COMMON.FFIELD' - include 'COMMON.MINIM' - include 'COMMON.INTERACT' -c - include 'COMMON.DISTFIT' - integer iff(maxres) - double precision time0,time1 - double precision energy(0:n_ene),ee - double precision var(maxvar) - integer ieval -c - logical debug,ltest,fail - character*50 linia -c - linia='test' - debug=.true. - in_pdb=0 - - - -c------------------------ -c -c freeze sec.elements -c - do i=1,nres - mask_phi(i)=1 - mask_theta(i)=1 - mask_side(i)=1 - iff(i)=0 - enddo - - do j=1,nbfrag - do i=bfrag(1,j),bfrag(2,j) - mask_phi(i)=0 - mask_theta(i)=0 - iff(i)=1 - enddo - if (bfrag(3,j).le.bfrag(4,j)) then - do i=bfrag(3,j),bfrag(4,j) - mask_phi(i)=0 - mask_theta(i)=0 - iff(i)=1 - enddo - else - do i=bfrag(4,j),bfrag(3,j) - mask_phi(i)=0 - mask_theta(i)=0 - iff(i)=1 - enddo - endif - enddo - do j=1,nhfrag - do i=hfrag(1,j),hfrag(2,j) - mask_phi(i)=0 - mask_theta(i)=0 - iff(i)=1 - enddo - enddo - mask_r=.true. - - - - nhpb0=nhpb -c -c store dist. constrains -c - do i=1,nres-3 - do j=i+3,nres - if ( iff(i).eq.1.and.iff(j).eq.1 ) then - nhpb=nhpb+1 - ihpb(nhpb)=i - jhpb(nhpb)=j - forcon(nhpb)=0.1 - dhpb(nhpb)=DIST(i,j) - endif - enddo - enddo - call hpb_partition - - if (debug) then - call chainbuild - call write_pdb(100+in_pdb,'input reg. structure',0d0) - endif - - - ipot0=ipot - maxmin0=maxmin - maxfun0=maxfun - wstrain0=wstrain - wang0=wang -c -c run soft pot. optimization -c - ipot=6 - wang=3.0 - maxmin=2000 - maxfun=4000 - call geom_to_var(nvar,var) -#ifdef MPI - time0=MPI_WTIME() -#else - time0=tcpu() -#endif - call minimize(etot,var,iretcode,nfun) - - write(iout,*)'SUMSL return code is',iretcode,' eval SOFT',nfun -#ifdef MPI - time1=MPI_WTIME() -#else - time1=tcpu() -#endif - write (iout,'(a,f6.2,f8.2,a)')' Time for soft min.',time1-time0, - & nfun/(time1-time0),' SOFT eval/s' - if (debug) then - call var_to_geom(nvar,var) - call chainbuild - call write_pdb(300+in_pdb,'soft structure',etot) - endif -c -c run full UNRES optimization with constrains and frozen 2D -c the same variables as soft pot. optimizatio -c - ipot=ipot0 - wang=wang0 - maxmin=maxmin0 - maxfun=maxfun0 -#ifdef MPI - time0=MPI_WTIME() -#else - time0=tcpu() -#endif - call minimize(etot,var,iretcode,nfun) - write(iout,*)'SUMSL MASK DIST return code is',iretcode, - & ' eval ',nfun - ieval=nfun - -#ifdef MPI - time1=MPI_WTIME() -#else - time1=tcpu() -#endif - write (iout,'(a,f6.2,f8.2,a)') - & ' Time for mask dist min.',time1-time0, - & nfun/(time1-time0),' eval/s' - if (debug) then - call var_to_geom(nvar,var) - call chainbuild - call write_pdb(400+in_pdb,'mask & dist',etot) - endif -c -c switch off constrains and -c run full UNRES optimization with frozen 2D -c - -c -c reset constrains -c - nhpb_c=nhpb - nhpb=nhpb0 - link_start=1 - link_end=nhpb - wstrain=wstrain0 - - -#ifdef MPI - time0=MPI_WTIME() -#else - time0=tcpu() -#endif - call minimize(etot,var,iretcode,nfun) - write(iout,*)'SUMSL MASK return code is',iretcode,' eval ',nfun - ieval=ieval+nfun - -#ifdef MPI - time1=MPI_WTIME() -#else - time1=tcpu() -#endif - write (iout,'(a,f6.2,f8.2,a)')' Time for mask min.',time1-time0, - & nfun/(time1-time0),' eval/s' - - - if (debug) then - call var_to_geom(nvar,var) - call chainbuild - call write_pdb(500+in_pdb,'mask 2d frozen',etot) - endif - - mask_r=.false. - - -c -c run full UNRES optimization with constrains and NO frozen 2D -c - - nhpb=nhpb_c - link_start=1 - link_end=nhpb - maxfun=maxfun0/5 - - do ico=1,5 - - wstrain=wstrain0/ico - -#ifdef MPI - time0=MPI_WTIME() -#else - time0=tcpu() -#endif - call minimize(etot,var,iretcode,nfun) - write(iout,'(a10,f6.3,a14,i3,a6,i5)') - & ' SUMSL DIST',wstrain,' return code is',iretcode, - & ' eval ',nfun - ieval=nfun - -#ifdef MPI - time1=MPI_WTIME() -#else - time1=tcpu() -#endif - write (iout,'(a,f6.2,f8.2,a)') - & ' Time for dist min.',time1-time0, - & nfun/(time1-time0),' eval/s' - if (debug) then - call var_to_geom(nvar,var) - call chainbuild - call write_pdb(600+in_pdb+ico,'dist cons',etot) - endif - - enddo -c - nhpb=nhpb0 - link_start=1 - link_end=nhpb - wstrain=wstrain0 - maxfun=maxfun0 - - -c - if (minim) then -#ifdef MPI - time0=MPI_WTIME() -#else - time0=tcpu() -#endif - call minimize(etot,var,iretcode,nfun) - write(iout,*)'------------------------------------------------' - write(iout,*)'SUMSL return code is',iretcode,' eval ',nfun, - & '+ DIST eval',ieval - -#ifdef MPI - time1=MPI_WTIME() -#else - time1=tcpu() -#endif - write (iout,'(a,f6.2,f8.2,a)')' Time for full min.',time1-time0, - & nfun/(time1-time0),' eval/s' - - - call var_to_geom(nvar,var) - call chainbuild - call write_pdb(999,'full min',etot) - endif - - return - end - - - subroutine beta_slide(i1,i2,i3,i4,i5,ieval,ij) - implicit real*8 (a-h,o-z) - include 'DIMENSIONS' -#ifdef MPI - include 'mpif.h' -#endif - include 'COMMON.GEO' - include 'COMMON.VAR' - include 'COMMON.INTERACT' - include 'COMMON.IOUNITS' - include 'COMMON.DISTFIT' - include 'COMMON.SBRIDGE' - include 'COMMON.CONTROL' - include 'COMMON.FFIELD' - include 'COMMON.MINIM' - include 'COMMON.CHAIN' - double precision time0,time1 - double precision energy(0:n_ene),ee - double precision var(maxvar) - integer jdata(5),isec(maxres) -c - jdata(1)=i1 - jdata(2)=i2 - jdata(3)=i3 - jdata(4)=i4 - jdata(5)=i5 - - call secondary2(.false.) - - do i=1,nres - isec(i)=0 - enddo - do j=1,nbfrag - do i=bfrag(1,j),bfrag(2,j) - isec(i)=1 - enddo - do i=bfrag(4,j),bfrag(3,j),sign(1,bfrag(3,j)-bfrag(4,j)) - isec(i)=1 - enddo - enddo - do j=1,nhfrag - do i=hfrag(1,j),hfrag(2,j) - isec(i)=2 - enddo - enddo - -c -c cut strands at the ends -c - if (jdata(2)-jdata(1).gt.3) then - jdata(1)=jdata(1)+1 - jdata(2)=jdata(2)-1 - if (jdata(3).lt.jdata(4)) then - jdata(3)=jdata(3)+1 - jdata(4)=jdata(4)-1 - else - jdata(3)=jdata(3)-1 - jdata(4)=jdata(4)+1 - endif - endif - -cv call chainbuild -cv call etotal(energy(0)) -cv etot=energy(0) -cv write(iout,*) nnt,nct,etot -cv call write_pdb(ij*100,'first structure',etot) -cv write(iout,*) 'N16 test',(jdata(i),i=1,5) - -c------------------------ -c generate constrains -c - ishift=jdata(5)-2 - if(ishift.eq.0) ishift=-2 - nhpb0=nhpb - call chainbuild - do i=jdata(1),jdata(2) - isec(i)=-1 - if(jdata(4).gt.jdata(3))then - do j=jdata(3)+i-jdata(1)-2,jdata(3)+i-jdata(1)+2 - isec(j)=-1 -cd print *,i,j,j+ishift - nhpb=nhpb+1 - ihpb(nhpb)=i - jhpb(nhpb)=j - forcon(nhpb)=1000.0 - dhpb(nhpb)=DIST(i,j+ishift) - enddo - else - do j=jdata(3)-i+jdata(1)+2,jdata(3)-i+jdata(1)-2,-1 - isec(j)=-1 -cd print *,i,j,j+ishift - nhpb=nhpb+1 - ihpb(nhpb)=i - jhpb(nhpb)=j - forcon(nhpb)=1000.0 - dhpb(nhpb)=DIST(i,j+ishift) - enddo - endif - enddo - - do i=nnt,nct-2 - do j=i+2,nct - if(isec(i).gt.0.or.isec(j).gt.0) then -cd print *,i,j - nhpb=nhpb+1 - ihpb(nhpb)=i - jhpb(nhpb)=j - forcon(nhpb)=0.1 - dhpb(nhpb)=DIST(i,j) - endif - enddo - enddo - - call hpb_partition - - call geom_to_var(nvar,var) - maxfun0=maxfun - wstrain0=wstrain - maxfun=4000/5 - - do ico=1,5 - - wstrain=wstrain0/ico - - call minimize(etot,var,iretcode,nfun) - write(iout,'(a10,f6.3,a14,i3,a6,i5)') - & ' SUMSL DIST',wstrain,' return code is',iretcode, - & ' eval ',nfun - ieval=ieval+nfun - - enddo -c - nhpb=nhpb0 - call hpb_partition - wstrain=wstrain0 - maxfun=maxfun0 -c -cd print *,etot - wscloc0=wscloc - wscloc=10.0 - call sc_move(nnt,nct,100,100d0,nft_sc,etot) - wscloc=wscloc0 -cv call chainbuild -cv call etotal(energy(0)) -cv etot=energy(0) -cv call write_pdb(ij*100+10,'sc_move',etot) -cd call intout -cd print *,nft_sc,etot - - return - end - - subroutine beta_zip(i1,i2,ieval,ij) - implicit real*8 (a-h,o-z) - include 'DIMENSIONS' -#ifdef MPI - include 'mpif.h' -#endif - include 'COMMON.GEO' - include 'COMMON.VAR' - include 'COMMON.INTERACT' - include 'COMMON.IOUNITS' - include 'COMMON.DISTFIT' - include 'COMMON.SBRIDGE' - include 'COMMON.CONTROL' - include 'COMMON.FFIELD' - include 'COMMON.MINIM' - include 'COMMON.CHAIN' - double precision time0,time1 - double precision energy(0:n_ene),ee - double precision var(maxvar) - character*10 test - -cv call chainbuild -cv call etotal(energy(0)) -cv etot=energy(0) -cv write(test,'(2i5)') i1,i2 -cv call write_pdb(ij*100,test,etot) -cv write(iout,*) 'N17 test',i1,i2,etot,ij - -c -c generate constrains -c - nhpb0=nhpb - nhpb=nhpb+1 - ihpb(nhpb)=i1 - jhpb(nhpb)=i2 - forcon(nhpb)=1000.0 - dhpb(nhpb)=4.0 - - call hpb_partition - - call geom_to_var(nvar,var) - maxfun0=maxfun - wstrain0=wstrain - maxfun=1000/5 - - do ico=1,5 - wstrain=wstrain0/ico - call minimize(etot,var,iretcode,nfun) - write(iout,'(a10,f6.3,a14,i3,a6,i5)') - & ' SUMSL DIST',wstrain,' return code is',iretcode, - & ' eval ',nfun - ieval=ieval+nfun -c do not comment the next line - call var_to_geom(nvar,var) -cv call chainbuild -cv call write_pdb(ij*100+ico,'dist cons',etot) - enddo - - nhpb=nhpb0 - call hpb_partition - wstrain=wstrain0 - maxfun=maxfun0 - -cv call etotal(energy(0)) -cv etot=energy(0) -cv write(iout,*) 'N17 test end',i1,i2,etot,ij - - - return - end