From 3b22160e2e6f9fec0d20501ae319870af6bd22b9 Mon Sep 17 00:00:00 2001 From: Cezary Czaplewski Date: Sat, 14 Mar 2020 20:29:50 +0100 Subject: [PATCH] update from Adam --- source/unres/src-HCD-5D/MD_A-MTS.F | 1 + source/unres/src-HCD-5D/TODO.AFTER.CASP14 | 2 + source/unres/src-HCD-5D/contact.f | 2 + source/unres/src-HCD-5D/elecont.f | 16 +- source/unres/src-HCD-5D/lagrangian_lesyng.F | 2 +- source/unres/src-HCD-5D/map.f | 93 -------- source/unres/src-HCD-5D/minimize_p.F | 2 +- source/wham/src-M-SAXS-homology/readpdb.f | 303 --------------------------- 8 files changed, 18 insertions(+), 403 deletions(-) delete mode 100644 source/unres/src-HCD-5D/map.f delete mode 100644 source/wham/src-M-SAXS-homology/readpdb.f diff --git a/source/unres/src-HCD-5D/MD_A-MTS.F b/source/unres/src-HCD-5D/MD_A-MTS.F index 1bc0eb2..76bec98 100644 --- a/source/unres/src-HCD-5D/MD_A-MTS.F +++ b/source/unres/src-HCD-5D/MD_A-MTS.F @@ -2312,6 +2312,7 @@ c write (iout,*) "ichain",ichain," innt",innt," inct",inct enddo end if enddo + d_t(:,nct)=0.0d0 c d_a(:,0)=d_a(:,1) c d_a(:,1)=0.0d0 c write (iout,*) "Shifting accelerations" diff --git a/source/unres/src-HCD-5D/TODO.AFTER.CASP14 b/source/unres/src-HCD-5D/TODO.AFTER.CASP14 index 85ea11a..cacb8a0 100644 --- a/source/unres/src-HCD-5D/TODO.AFTER.CASP14 +++ b/source/unres/src-HCD-5D/TODO.AFTER.CASP14 @@ -5,3 +5,5 @@ 4. HREMD 5. Fourbody interactions - eliminate pp-contact etc. storage (currently 4body switched off by default, -DFOURBODY flag switches on). +6. Fix LBFGS - the linesearch (search) subroutine does not handle difficult + cases when changing variables can result in nans. diff --git a/source/unres/src-HCD-5D/contact.f b/source/unres/src-HCD-5D/contact.f index cc4e0b7..695446f 100644 --- a/source/unres/src-HCD-5D/contact.f +++ b/source/unres/src-HCD-5D/contact.f @@ -114,11 +114,13 @@ c---------------------------------------------------------------------------- kkk=0 c print *,'nnt=',nnt,' nct=',nct do i=nnt,nct-3 + if (itype(i).eq.ntyp1) cycle do k=1,3 c(k,2*nres+1)=0.5d0*(c(k,i)+c(k,i+1)) enddo do j=i+2,nct-1 do k=1,3 + if (itype(j).eq.ntyp1) cycle c(k,2*nres+2)=0.5d0*(c(k,j)+c(k,j+1)) enddo if (dist(2*nres+1,2*nres+2).lt.rcomp) then diff --git a/source/unres/src-HCD-5D/elecont.f b/source/unres/src-HCD-5D/elecont.f index f43b037..00ce016 100644 --- a/source/unres/src-HCD-5D/elecont.f +++ b/source/unres/src-HCD-5D/elecont.f @@ -12,6 +12,7 @@ double precision app_(2,2),bpp_(2,2),rpp_(2,2) integer ncont,icont(2,maxcont) double precision econt(maxcont) + integer xshift,yshift,zshift * * Load the constants of peptide bond - peptide bond interactions. * Type 1 - ordinary peptide bond, type 2 - alkylated peptide bond (e.g. @@ -52,12 +53,14 @@ c data epp / 0.3045d0, 0.3649d0, 0.3649d0, 0.5743d0/ xmedi=xi+0.5*dxi ymedi=yi+0.5*dyi zmedi=zi+0.5*dzi +c write (iout,*) "i",xmedi,ymedi,zmedi xmedi=mod(xmedi,boxxsize) if (xmedi.lt.0) xmedi=xmedi+boxxsize ymedi=mod(ymedi,boxysize) if (ymedi.lt.0) ymedi=ymedi+boxysize zmedi=mod(zmedi,boxzsize) if (zmedi.lt.0) zmedi=zmedi+boxzsize +c write (iout,*) "i",xmedi,ymedi,zmedi do 4 j=i+2,nct-1 if (itype(j).eq.ntyp1 .or. itype(j+1).eq.ntyp1) goto 4 ind=ind+1 @@ -75,15 +78,16 @@ c data epp / 0.3045d0, 0.3649d0, 0.3649d0, 0.5743d0/ xj=c(1,j)+0.5*dxj yj=c(2,j)+0.5*dyj zj=c(3,j)+0.5*dzj +c write (iout,*) "j",xj,yj,zj xj=mod(xj,boxxsize) if (xj.lt.0) xj=xj+boxxsize yj=mod(yj,boxysize) if (yj.lt.0) yj=yj+boxysize zj=mod(zj,boxzsize) if (zj.lt.0) zj=zj+boxzsize - dist_init=(xj-xi)**2+(yj-yi)**2+(zj-zi)**2 - write (iout,*) "i",i,xi,yi,zi," j",j,xj,yj,xj,"dist", - & dsqrt(dist_init) +c write (iout,*) "j",xj,yj,zj + dist_init=(xj-xmedi)**2+(yj-ymedi)**2+(zj-zmedi)**2 +c write (iout,*) "dist",dsqrt(dist_init) xj_safe=xj yj_safe=yj zj_safe=zj @@ -94,7 +98,9 @@ c data epp / 0.3045d0, 0.3649d0, 0.3649d0, 0.5743d0/ xj=xj_safe+xshift*boxxsize yj=yj_safe+yshift*boxysize zj=zj_safe+zshift*boxzsize - dist_temp=(xj-xi)**2+(yj-yi)**2+(zj-zi)**2 + dist_temp=(xj-xmedi)**2+(yj-ymedi)**2+(zj-zmedi)**2 +c write (iout,*) "shift",xshift,yshift,zshift," dist_temp", +c & dist_temp," dist_init",dist_init if(dist_temp.lt.dist_init) then dist_init=dist_temp xj_temp=xj @@ -143,7 +149,7 @@ c data epp / 0.3045d0, 0.3649d0, 0.3649d0, 0.5743d0/ endif ees=ees+eesij evdw=evdw+evdwij*sss - write (iout,*) "i"," j",j," rij",dsqrt(rij)," eesij",eesij +c write (iout,*) "i"," j",j," rij",dsqrt(rij)," eesij",eesij 4 continue 1 continue if (lprint) then diff --git a/source/unres/src-HCD-5D/lagrangian_lesyng.F b/source/unres/src-HCD-5D/lagrangian_lesyng.F index 5de830f..6a6967a 100644 --- a/source/unres/src-HCD-5D/lagrangian_lesyng.F +++ b/source/unres/src-HCD-5D/lagrangian_lesyng.F @@ -38,7 +38,7 @@ c------------------------------------------------------------------------- integer i,j,ind double precision zapas(MAXRES6),muca_factor - logical lprn /.false./ + logical lprn /.true./ integer itime common /cipiszcze/ itime #ifdef FIVEDIAG diff --git a/source/unres/src-HCD-5D/map.f b/source/unres/src-HCD-5D/map.f deleted file mode 100644 index ed374db..0000000 --- a/source/unres/src-HCD-5D/map.f +++ /dev/null @@ -1,93 +0,0 @@ - subroutine map - implicit none - include 'DIMENSIONS' - include 'COMMON.MAP' - include 'COMMON.VAR' - include 'COMMON.GEO' - include 'COMMON.DERIV' - include 'COMMON.IOUNITS' - include 'COMMON.NAMES' - include 'COMMON.CONTROL' - include 'COMMON.TORCNSTR' - double precision energia(0:n_ene) - character*5 angid(4) /'PHI','THETA','ALPHA','OMEGA'/ - double precision ang_list(10) - double precision g(maxvar),x(maxvar),gnorm,etot - integer i,ii,iii,j,k,nf,nfun,iretcode,nmax,ntot - integer uiparm(1) - double precision urparm(1),fdum - external fdum - integer nn(10) - write (iout,'(a,i3,a)')'Energy map constructed in the following ', - & nmap,' groups of variables:' - do i=1,nmap - write (iout,'(2a,i3,a,i3)') angid(kang(i)),' of residues ', - & res1(i),' to ',res2(i) - enddo - nmax=nstep(1) - do i=2,nmap - if (nmax.lt.nstep(i)) nmax=nstep(i) - enddo - ntot=nmax**nmap - iii=0 - write (istat,'(1h#,a14,29a15)') (" ",k=1,nmap), - & (ename(print_order(k)),k=1,nprint_ene),"ETOT","GNORM" - do i=0,ntot-1 - ii=i - do j=1,nmap - nn(j)=mod(ii,nmax)+1 - ii=ii/nmax - enddo - do j=1,nmap - if (nn(j).gt.nstep(j)) goto 10 - enddo - iii=iii+1 -Cd write (iout,*) i,iii,(nn(j),j=1,nmap) - do j=1,nmap - ang_list(j)=ang_from(j) - & +(nn(j)-1)*(ang_to(j)-ang_from(j))/nstep(j) - do k=res1(j),res2(j) - goto (1,2,3,4), kang(j) - 1 phi(k)=deg2rad*ang_list(j) - if (minim) phi0(k-res1(j)+1)=deg2rad*ang_list(j) - goto 5 - 2 theta(k)=deg2rad*ang_list(j) - goto 5 - 3 alph(k)=deg2rad*ang_list(j) - goto 5 - 4 omeg(k)=deg2rad*ang_list(j) - 5 continue - enddo ! k - enddo ! j - call chainbuild - if (minim) then - call geom_to_var(nvar,x) - call minimize(etot,x,iretcode,nfun) - print *,'SUMSL return code is',iretcode,' eval ',nfun -c call intout - else - call zerograd - call geom_to_var(nvar,x) - endif - call etotal(energia(0)) - etot = energia(0) - nf=1 - nfl=3 - call gradient(nvar,x,nf,g,uiparm,urparm,fdum) - gnorm=0.0d0 - do k=1,nvar - gnorm=gnorm+g(k)**2 - enddo - etot=energia(0) - - gnorm=dsqrt(gnorm) -c write (iout,'(6(1pe15.5))') (ang_list(k),k=1,nmap),etot,gnorm - write (istat,'(30e15.5)') (ang_list(k),k=1,nmap), - & (energia(print_order(ii)),ii=1,nprint_ene),etot,gnorm -c write (iout,*) 'POINT',I,' ANGLES:',(ang_list(k),k=1,nmap) -c call intout -c call enerprint(energia) - 10 continue - enddo ! i - return - end diff --git a/source/unres/src-HCD-5D/minimize_p.F b/source/unres/src-HCD-5D/minimize_p.F index 6b9d204..377bc47 100644 --- a/source/unres/src-HCD-5D/minimize_p.F +++ b/source/unres/src-HCD-5D/minimize_p.F @@ -34,7 +34,7 @@ external funcgrad external optsave #else - dimension iv(liv) + integer iv(liv) double precision v(1:lv) common /przechowalnia/ v integer idum diff --git a/source/wham/src-M-SAXS-homology/readpdb.f b/source/wham/src-M-SAXS-homology/readpdb.f deleted file mode 100644 index b6dbd6e..0000000 --- a/source/wham/src-M-SAXS-homology/readpdb.f +++ /dev/null @@ -1,303 +0,0 @@ - subroutine readpdb -C Read the PDB file and convert the peptide geometry into virtual-chain -C geometry. - implicit none - include 'DIMENSIONS' - include 'DIMENSIONS.ZSCOPT' - include 'COMMON.CONTROL' - include 'COMMON.LOCAL' - include 'COMMON.VAR' - include 'COMMON.CHAIN' - include 'COMMON.INTERACT' - include 'COMMON.IOUNITS' - include 'COMMON.GEO' - include 'COMMON.NAMES' - include 'COMMON.SBRIDGE' - character*3 seq,atom,res - character*80 card - double precision sccor(3,50) - integer i,j,iii,ibeg,ishift,ishift1,ity,ires,ires_old - double precision dcj - integer rescode,kkk,lll,icha,cou,kupa,iprzes - ibeg=1 - ishift1=0 - do - read (ipdbin,'(a80)',end=10) card - if (card(:3).eq.'END') then - goto 10 - else if (card(:3).eq.'TER') then -C End current chain -c ires_old=ires+1 - ires_old=ires+2 - itype(ires_old-1)=ntyp1 - itype(ires_old)=ntyp1 - ibeg=2 -c write (iout,*) "Chain ended",ires,ishift,ires_old - call sccenter(ires,iii,sccor) - endif -C Fish out the ATOM cards. - if (index(card(1:4),'ATOM').gt.0) then - read (card(14:16),'(a3)') atom - if (atom.eq.'CA' .or. atom.eq.'CH3') then -C Calculate the CM of the preceding residue. - if (ibeg.eq.0) then - call sccenter(ires,iii,sccor) - endif -C Start new residue. -c write (iout,'(a80)') card - read (card(23:26),*) ires - read (card(18:20),'(a3)') res - if (ibeg.eq.1) then - ishift=ires-1 - if (res.ne.'GLY' .and. res.ne. 'ACE') then - ishift=ishift-1 - itype(1)=ntyp1 - endif -c write (iout,*) "ires",ires," ibeg",ibeg," ishift",ishift - ibeg=0 - else if (ibeg.eq.2) then -c Start a new chain - ishift=-ires_old+ires-1 -c write (iout,*) "New chain started",ires,ishift - ibeg=0 - endif - ires=ires-ishift -c write (2,*) "ires",ires," ishift",ishift - if (res.eq.'ACE') then - ity=10 - else - itype(ires)=rescode(ires,res,0) - endif - read(card(31:54),'(3f8.3)') (c(j,ires),j=1,3) - read(card(61:66),*) bfac(ires) - write (iout,'(2i3,2x,a,3f8.3,5x,f8.3)') - & ires,itype(ires),res,(c(j,ires),j=1,3),bfac(ires) - iii=1 - do j=1,3 - sccor(j,iii)=c(j,ires) - enddo - else if (atom.ne.'O '.and.atom(1:1).ne.'H' .and. - & atom(1:1).ne.'Q' .and. atom(1:2).ne.'1H' .and. - & atom(1:2).ne.'2H' .and. atom(1:2).ne.'3H' .and. - & atom.ne.'N ' .and. atom.ne.'C ') then - iii=iii+1 - read(card(31:54),'(3f8.3)') (sccor(j,iii),j=1,3) - endif - endif - enddo - 10 write (iout,'(a,i5)') ' Nres: ',ires -C Calculate dummy residue coordinates inside the "chain" of a multichain -C system - nres=ires - do i=2,nres-1 -c write (iout,*) i,itype(i) - - if (itype(i).eq.ntyp1) then - if (itype(i+1).eq.ntyp1) then -C 16/01/2014 by Adasko: Adding to dummy atoms in the chain -C first is connected prevous chain (itype(i+1).eq.ntyp1)=true -C second dummy atom is conected to next chain itype(i+1).eq.ntyp1=false -C if (unres_pdb) then -C 2/15/2013 by Adam: corrected insertion of the last dummy residue -C call refsys(i-3,i-2,i-1,e1,e2,e3,fail) -C if (fail) then -C e2(1)=0.0d0 -C e2(2)=1.0d0 -C e2(3)=0.0d0 -C endif !fail -C do j=1,3 -C c(j,i)=c(j,i-1)-1.9d0*e2(j) -C enddo -C else !unres_pdb - do j=1,3 - dcj=(c(j,i-2)-c(j,i-3))/2.0 - c(j,i)=c(j,i-1)+dcj - c(j,nres+i)=c(j,i) - enddo -C endif !unres_pdb - else !itype(i+1).eq.ntyp1 -C if (unres_pdb) then -C 2/15/2013 by Adam: corrected insertion of the first dummy residue -C call refsys(i+1,i+2,i+3,e1,e2,e3,fail) -C if (fail) then -C e2(1)=0.0d0 -C e2(2)=1.0d0 -C e2(3)=0.0d0 -C endif -C do j=1,3 -C c(j,i)=c(j,i+1)-1.9d0*e2(j) -C enddo -C else !unres_pdb - do j=1,3 - dcj=(c(j,i+3)-c(j,i+2))/2.0 - c(j,i)=c(j,i+1)-dcj - c(j,nres+i)=c(j,i) - enddo -C endif !unres_pdb - endif !itype(i+1).eq.ntyp1 - endif !itype.eq.ntyp1 - enddo -C Calculate the CM of the last side chain. - call sccenter(ires,iii,sccor) - nsup=nres - nstart_sup=1 - if (itype(nres).ne.10) then - nres=nres+1 - itype(nres)=ntyp1 - do j=1,3 - dcj=(c(j,nres-2)-c(j,nres-3))/2.0 - c(j,nres)=c(j,nres-1)+dcj - c(j,2*nres)=c(j,nres) - enddo - endif - do i=2,nres-1 - do j=1,3 - c(j,i+nres)=dc(j,i) - enddo - enddo - do j=1,3 - c(j,nres+1)=c(j,1) - c(j,2*nres)=c(j,nres) - enddo - if (itype(1).eq.ntyp1) then - nsup=nsup-1 - nstart_sup=2 - do j=1,3 - dcj=(c(j,4)-c(j,3))/2.0 - c(j,1)=c(j,2)-dcj - c(j,nres+1)=c(j,1) - enddo - endif -C Calculate internal coordinates. - do ires=1,nres - write (iout,'(2i3,2x,a,3f8.3,5x,3f8.3)') - & ires,itype(ires),restyp(itype(ires)),(c(j,ires),j=1,3), - & (c(j,nres+ires),j=1,3) - enddo - call int_from_cart(.true.,.false.) - write (iout,*) "After int_from_cart" - call flush(iout) - do i=1,nres-1 - do j=1,3 - dc(j,i)=c(j,i+1)-c(j,i) - dc_norm(j,i)=dc(j,i)*vbld_inv(i+1) - enddo - enddo - do i=2,nres-1 - do j=1,3 - dc(j,i+nres)=c(j,i+nres)-c(j,i) - dc_norm(j,i+nres)=dc(j,i+nres)*vbld_inv(i+nres) - enddo -c write (iout,*) i,(dc(j,i+nres),j=1,3),(dc_norm(j,i+nres),j=1,3), -c & vbld_inv(i+nres) - enddo -c call chainbuild -C Copy the coordinates to reference coordinates - do i=1,nres - do j=1,3 - cref(j,i)=c(j,i) - cref(j,i+nres)=c(j,i+nres) - enddo - enddo - 100 format (//' alpha-carbon coordinates ', - & ' centroid coordinates'/ - 1 ' ', 6X,'X',11X,'Y',11X,'Z', - & 10X,'X',11X,'Y',11X,'Z') - 110 format (a,'(',i3,')',6f12.5) - - ishift_pdb=ishift - return - end -c--------------------------------------------------------------------------- - subroutine int_from_cart(lside,lprn) - implicit none - include 'DIMENSIONS' - include 'DIMENSIONS.ZSCOPT' - include 'COMMON.LOCAL' - include 'COMMON.VAR' - include 'COMMON.CHAIN' - include 'COMMON.INTERACT' - include 'COMMON.IOUNITS' - include 'COMMON.GEO' - include 'COMMON.NAMES' - character*3 seq,atom,res - character*80 card - double precision sccor(3,50) - integer rescode - double precision dist,alpha,beta,di - integer i,j,iti - logical lside,lprn - if (lprn) then - write (iout,'(/a)') - & 'Internal coordinates calculated from crystal structure.' - if (lside) then - write (iout,'(8a)') ' Res ',' dvb',' Theta', - & ' Phi',' Dsc_id',' Dsc',' Alpha', - & ' Omega' - else - write (iout,'(4a)') ' Res ',' dvb',' Theta', - & ' Phi' - endif - endif - do i=2,nres - iti=itype(i) -c write (iout,*) i,i-1,(c(j,i),j=1,3),(c(j,i-1),j=1,3),dist(i,i-1) - if (itype(i-1).ne.ntyp1 .and. itype(i).ne.ntyp1 .and. - & (dist(i,i-1).lt.1.0D0 .or. dist(i,i-1).gt.6.0D0)) then - write (iout,'(a,i4)') 'Bad Cartesians for residue',i - stop - endif - theta(i+1)=alpha(i-1,i,i+1) - if (i.gt.2) phi(i+1)=beta(i-2,i-1,i,i+1) - enddo - if (itype(1).eq.ntyp1) then - do j=1,3 - c(j,1)=c(j,2)+(c(j,3)-c(j,4)) - enddo - endif - if (itype(nres).eq.ntyp1) then - do j=1,3 - c(j,nres)=c(j,nres-1)+(c(j,nres-2)-c(j,nres-3)) - enddo - endif - if (lside) then - do i=2,nres-1 - do j=1,3 - c(j,maxres2)=0.5D0*(c(j,i-1)+c(j,i+1)) - enddo - iti=itype(i) - di=dist(i,nres+i) - if (iti.ne.10) then - alph(i)=alpha(nres+i,i,maxres2) - omeg(i)=beta(nres+i,i,maxres2,i+1) - endif - if (lprn) - & write (iout,'(a3,i4,7f10.3)') restyp(iti),i,dist(i,i-1), - & rad2deg*theta(i),rad2deg*phi(i),dsc(iti),di, - & rad2deg*alph(i),rad2deg*omeg(i) - enddo - else if (lprn) then - do i=2,nres - iti=itype(i) - write (iout,'(a3,i4,7f10.3)') restyp(iti),i,dist(i,i-1), - & rad2deg*theta(i),rad2deg*phi(i) - enddo - endif - return - end -c--------------------------------------------------------------------------- - subroutine sccenter(ires,nscat,sccor) - implicit none - include 'DIMENSIONS' - include 'COMMON.CHAIN' - integer ires,nscat,i,j - double precision sccor(3,50),sccmj - do j=1,3 - sccmj=0.0D0 - do i=1,nscat - sccmj=sccmj+sccor(j,i) - enddo - dc(j,ires)=sccmj/nscat - enddo - return - end -- 1.7.9.5