X-Git-Url: http://mmka.chem.univ.gda.pl/gitweb/?a=blobdiff_plain;f=source%2Funres%2Fio_config.f90;h=3f4303ac0a17a5e96f77b87baf4ce8af642b1d10;hb=705644e0cbb7678faefd6fe1bc436159d38ad85d;hp=6f51253ae424dd92489f79cdf57e9a9ccdafa232;hpb=4367d241fbb2bc284580092d2d177b7c79ac3a42;p=unres4.git diff --git a/source/unres/io_config.f90 b/source/unres/io_config.f90 index 6f51253..3f4303a 100644 --- a/source/unres/io_config.f90 +++ b/source/unres/io_config.f90 @@ -735,11 +735,11 @@ character(len=1) :: toronelet(-2:2) = (/"p","a","G","A","P"/) logical :: lprint,LaTeX real(kind=8),dimension(3,3,maxlob) :: blower !(3,3,maxlob) - real(kind=8),dimension(13) :: b + real(kind=8),dimension(13) :: buse character(len=3) :: lancuch !,ucase !el local variables integer :: m,n,l,i,j,k,iblock,lll,llll,ll,nlobi,mm - integer :: maxinter,junk,kk,ii + integer :: maxinter,junk,kk,ii,ncatprotparm real(kind=8) :: v0ijsccor,v0ijsccor1,v0ijsccor2,v0ijsccor3,si,& dwa16,rjunk,akl,v0ij,rri,epsij,rrij,sigeps,sigt1sq,& sigt2sq,sigii1,sigii2,ratsig1,ratsig2,rsum_max,r_augm,& @@ -776,12 +776,12 @@ ! allocate(dsc(ntyp1)) !(ntyp1) allocate(dsc_inv(ntyp1)) !(ntyp1) + allocate(nbondterm_nucl(ntyp_molec(2))) !(ntyp) + allocate(vbldsc0_nucl(maxbondterm,ntyp_molec(2))) !(maxbondterm,ntyp) + allocate(aksc_nucl(maxbondterm,ntyp_molec(2))) !(maxbondterm,ntyp) allocate(nbondterm(ntyp)) !(ntyp) allocate(vbldsc0(maxbondterm,ntyp)) !(maxbondterm,ntyp) allocate(aksc(maxbondterm,ntyp)) !(maxbondterm,ntyp) - allocate(msc(ntyp+1)) !(ntyp+1) - allocate(isc(ntyp+1)) !(ntyp+1) - allocate(restok(ntyp+1)) !(ntyp+1) allocate(abond0(maxbondterm,ntyp)) !(maxbondterm,ntyp) allocate(long_r_sidechain(ntyp)) allocate(short_r_sidechain(ntyp)) @@ -789,6 +789,10 @@ dsc_inv(:)=0.0d0 #ifdef CRYST_BOND + allocate(msc(ntyp+1)) !(ntyp+1) + allocate(isc(ntyp+1)) !(ntyp+1) + allocate(restok(ntyp+1)) !(ntyp+1) + read (ibond,*) vbldp0,akp,mp,ip,pstok do i=1,ntyp nbondterm(i)=1 @@ -801,10 +805,14 @@ endif enddo #else - read (ibond,*) junk,vbldp0,vbldpDUM,akp,rjunk,mp,ip,pstok - do i=1,ntyp + allocate(msc(ntyp+1,5)) !(ntyp+1) + allocate(isc(ntyp+1,5)) !(ntyp+1) + allocate(restok(ntyp+1,5)) !(ntyp+1) + + read (ibond,*) junk,vbldp0,vbldpDUM,akp,rjunk,mp(1),ip(1),pstok(1) + do i=1,ntyp_molec(1) read (ibond,*) nbondterm(i),(vbldsc0(j,i),aksc(j,i),abond0(j,i),& - j=1,nbondterm(i)),msc(i),isc(i),restok(i) + j=1,nbondterm(i)),msc(i,1),isc(i,1),restok(i,1) dsc(i) = vbldsc0(1,i) if (i.eq.10) then dsc_inv(i)=0.0D0 @@ -813,20 +821,57 @@ endif enddo #endif + read (ibond_nucl,*) vbldp0_nucl,akp_nucl,mp(2),ip(2),pstok(2) + do i=1,ntyp_molec(2) + nbondterm_nucl(i)=1 + read (ibond_nucl,*) vbldsc0_nucl(1,i),aksc_nucl(1,i),msc(i,2),isc(i,2),restok(i,2) +! dsc(i) = vbldsc0_nucl(1,i) +! if (i.eq.10) then +! dsc_inv(i)=0.0D0 +! else +! dsc_inv(i)=1.0D0/dsc(i) +! endif + enddo +! read (ibond_nucl,*) junk,vbldp0_nucl,akp_nucl,rjunk,mp(2),ip(2),pstok(2) +! do i=1,ntyp_molec(2) +! read (ibond_nucl,*) nbondterm_nucl(i),(vbldsc0_nucl(j,i),& +! aksc_nucl(j,i),abond0_nucl(j,i),& +! j=1,nbondterm_nucl(i)),msc(i,2),isc(i,2),restok(i,2) +! dsc(i) = vbldsc0(1,i) +! if (i.eq.10) then +! dsc_inv(i)=0.0D0 +! else +! dsc_inv(i)=1.0D0/dsc(i) +! endif +! enddo + if (lprint) then write(iout,'(/a/)')"Dynamic constants of the interaction sites:" write (iout,'(a10,a3,6a10)') 'Type','N','VBL','K','A0','mass',& 'inertia','Pstok' - write(iout,'(a10,i3,6f10.5)') "p",1,vbldp0,akp,0.0d0,mp,ip,pstok + write(iout,'(a10,i3,6f10.5)') "p",1,vbldp0,akp,0.0d0,mp(1),ip(1),pstok(1) do i=1,ntyp - write (iout,'(a10,i3,6f10.5)') restyp(i),nbondterm(i),& - vbldsc0(1,i),aksc(1,i),abond0(1,i),msc(i),isc(i),restok(i) + write (iout,'(a10,i3,6f10.5)') restyp(i,1),nbondterm(i),& + vbldsc0(1,i),aksc(1,i),abond0(1,i),msc(i,1),isc(i,1),restok(i,1) do j=2,nbondterm(i) write (iout,'(13x,3f10.5)') & vbldsc0(j,i),aksc(j,i),abond0(j,i) enddo enddo endif + do i=1,ntyp_molec(5) + read(iion,*) msc(i,5),restok(i,5) + print *,msc(i,5),restok(i,5) + enddo + ip(5)=0.2 +! isc(5)=0.2 + read (iion,*) ncatprotparm + allocate(catprm(ncatprotparm,4)) + do k=1,4 + read (iion,*) (catprm(i,k),i=1,ncatprotparm) + enddo + print *, catprm +! read (iion,*) (vcatprm(k),k=1,ncatprotpram) !---------------------------------------------------- allocate(a0thet(-ntyp:ntyp),theta0(-ntyp:ntyp)) allocate(sig0(-ntyp:ntyp),sigc0(-ntyp:ntyp)) !(-ntyp:ntyp) @@ -912,7 +957,7 @@ ' ATHETA0 ',' A1 ',' A2 ',& ' B1 ',' B2 ' do i=1,ntyp - write(iout,'(a3,i4,2x,5(1pe14.5))') restyp(i),i,& + write(iout,'(a3,i4,2x,5(1pe14.5))') restyp(i,1),i,& a0thet(i),(athet(j,i,1,1),j=1,2),(bthet(j,i,1,1),j=1,2) enddo write (iout,'(/a/9x,5a/79(1h-))') & @@ -920,7 +965,7 @@ ' ALPH0 ',' ALPH1 ',' ALPH2 ',& ' ALPH3 ',' SIGMA0C ' do i=1,ntyp - write (iout,'(a3,i4,2x,5(1pe14.5))') restyp(i),i,& + write (iout,'(a3,i4,2x,5(1pe14.5))') restyp(i,1),i,& (polthet(j,i),j=0,3),sigc0(i) enddo write (iout,'(/a/9x,5a/79(1h-))') & @@ -928,7 +973,7 @@ ' THETA0 ',' SIGMA0 ',' G1 ',& ' G2 ',' G3 ' do i=1,ntyp - write (iout,'(a3,i4,2x,5(1pe14.5))') restyp(i),i,theta0(i),& + write (iout,'(a3,i4,2x,5(1pe14.5))') restyp(i,1),i,theta0(i),& sig0(i),(gthet(j,i),j=1,3) enddo else @@ -939,7 +984,7 @@ ' theta0 ',' a1*10^2 ',' a2*10^2 ',& ' b1*10^1 ',' b2*10^1 ' do i=1,ntyp - write(iout,'(a3,1h&,2x,5(f8.3,1h&))') restyp(i),& + write(iout,'(a3,1h&,2x,5(f8.3,1h&))') restyp(i,1),& a0thet(i),(100*athet(j,i,1,1),j=1,2),& (10*bthet(j,i,1,1),j=1,2) enddo @@ -948,7 +993,7 @@ ' alpha0 ',' alph1 ',' alph2 ',& ' alhp3 ',' sigma0c ' do i=1,ntyp - write (iout,'(a3,1h&,2x,5(1pe12.3,1h&))') restyp(i),& + write (iout,'(a3,1h&,2x,5(1pe12.3,1h&))') restyp(i,1),& (polthet(j,i),j=0,3),sigc0(i) enddo write (iout,'(/a/9x,5a/79(1h-))') & @@ -956,7 +1001,7 @@ ' theta0 ',' sigma0*10^2 ',' G1*10^-1',& ' G2 ',' G3*10^1 ' do i=1,ntyp - write (iout,'(a3,1h&,2x,5(f8.3,1h&))') restyp(i),theta0(i),& + write (iout,'(a3,1h&,2x,5(f8.3,1h&))') restyp(i,1),theta0(i),& 100*sig0(i),gthet(1,i)*0.1D0,gthet(2,i),gthet(3,i)*10.0D0 enddo endif @@ -1207,6 +1252,65 @@ close (ithep_pdb) #endif close(ithep) +!--------------- Reading theta parameters for nucleic acid------- + read (ithep_nucl,*,err=111,end=111) nthetyp_nucl,ntheterm_nucl,& + ntheterm2_nucl,ntheterm3_nucl,nsingle_nucl,ndouble_nucl + nntheterm_nucl=max0(ntheterm_nucl,ntheterm2_nucl,ntheterm3_nucl) + allocate(ithetyp_nucl(ntyp1_molec(2))) !(-ntyp1:ntyp1) + allocate(aa0thet_nucl(nthetyp_nucl+1,& + nthetyp_nucl+1,nthetyp_nucl+1)) +!(-maxthetyp1:maxthetyp1,-maxthetyp1:maxthetyp1,-maxthetyp1:maxthetyp1,2) + allocate(aathet_nucl(ntheterm_nucl+1,nthetyp_nucl+1,& + nthetyp_nucl+1,nthetyp_nucl+1)) +!(maxtheterm,-maxthetyp1:maxthetyp1,& +! -maxthetyp1:maxthetyp1,-maxthetyp1:maxthetyp1,2) + allocate(bbthet_nucl(nsingle_nucl+1,ntheterm2_nucl+1,nthetyp_nucl+1,& + nthetyp_nucl+1,nthetyp_nucl+1)) + allocate(ccthet_nucl(nsingle_nucl+1,ntheterm2_nucl+1,nthetyp_nucl+1,& + nthetyp_nucl+1,nthetyp_nucl+1)) + allocate(ddthet_nucl(nsingle_nucl+1,ntheterm2_nucl+1,nthetyp_nucl+1,& + nthetyp_nucl+1,nthetyp_nucl+1)) + allocate(eethet_nucl(nsingle_nucl+1,ntheterm2_nucl+1,nthetyp_nucl+1,& + nthetyp_nucl+1,nthetyp_nucl+1)) +!(maxsingle,maxtheterm2,-maxthetyp1:maxthetyp1,& +! -maxthetyp1:maxthetyp1,-maxthetyp1:maxthetyp1,2) + allocate(ffthet_nucl(ndouble_nucl+1,ndouble_nucl+1,ntheterm3_nucl+1,& + nthetyp_nucl+1,nthetyp_nucl+1,nthetyp_nucl+1)) + allocate(ggthet_nucl(ndouble_nucl+1,ndouble_nucl+1,ntheterm3_nucl+1,& + nthetyp_nucl+1,nthetyp_nucl+1,nthetyp_nucl+1)) + +!(maxdouble,maxdouble,maxtheterm3,-maxthetyp1:maxthetyp1,& +! -maxthetyp1:maxthetyp1,-maxthetyp1:maxthetyp1,2)) + + read (ithep_nucl,*,err=111,end=111) (ithetyp_nucl(i),i=1,ntyp1_molec(2)) + + aa0thet_nucl(:,:,:)=0.0d0 + aathet_nucl(:,:,:,:)=0.0d0 + bbthet_nucl(:,:,:,:,:)=0.0d0 + ccthet_nucl(:,:,:,:,:)=0.0d0 + ddthet_nucl(:,:,:,:,:)=0.0d0 + eethet_nucl(:,:,:,:,:)=0.0d0 + ffthet_nucl(:,:,:,:,:,:)=0.0d0 + ggthet_nucl(:,:,:,:,:,:)=0.0d0 + + do i=1,nthetyp_nucl + do j=1,nthetyp_nucl + do k=1,nthetyp_nucl + read (ithep_nucl,'(3a)',end=111,err=111) t1,t2,t3 + read (ithep_nucl,*,end=111,err=111) aa0thet_nucl(i,j,k) + read (ithep_nucl,*,end=111,err=111)(aathet_nucl(l,i,j,k),l=1,ntheterm_nucl) + read (ithep_nucl,*,end=111,err=111) & + (((bbthet_nucl(lll,ll,i,j,k),lll=1,nsingle_nucl), & + (ccthet_nucl(lll,ll,i,j,k),lll=1,nsingle_nucl), & + (ddthet_nucl(lll,ll,i,j,k),lll=1,nsingle_nucl), & + (eethet_nucl(lll,ll,i,j,k),lll=1,nsingle_nucl)),ll=1,ntheterm2_nucl) + read (ithep_nucl,*,end=111,err=111) & + (((ffthet_nucl(llll,lll,ll,i,j,k),ffthet_nucl(lll,llll,ll,i,j,k), & + ggthet_nucl(llll,lll,ll,i,j,k),ggthet_nucl(lll,llll,ll,i,j,k), & + llll=1,lll-1),lll=2,ndouble_nucl),ll=1,ntheterm3_nucl) + enddo + enddo + enddo !------------------------------------------- allocate(nlob(ntyp1)) !(ntyp1) @@ -1285,7 +1389,7 @@ nlobi=nlob(i) if (nlobi.gt.0) then if (LaTeX) then - write (iout,'(/3a,i2,a,f8.3)') 'Residue type: ',restyp(i),& + write (iout,'(/3a,i2,a,f8.3)') 'Residue type: ',restyp(i,1),& ' # of gaussian lobes:',nlobi,' dsc:',dsc(i) write (iout,'(1h&,a,3(2h&&,f8.3,2h&&))') & 'log h',(bsc(j,i),j=1,nlobi) @@ -1326,6 +1430,24 @@ enddo endif enddo +!---------reading nucleic acid parameters for rotamers------------------- + allocate(sc_parmin_nucl(9,ntyp_molec(2))) !(maxsccoef,ntyp) + do i=1,ntyp_molec(2) + read (irotam_nucl,*,end=112,err=112) + do j=1,9 + read(irotam_nucl,*,end=112,err=112) sc_parmin_nucl(j,i) + enddo + enddo + close(irotam_nucl) + if (lprint) then + write (iout,*) + write (iout,*) "Base rotamer parameters" + do i=1,ntyp_molec(2) + write (iout,'(a)') restyp(i,2) + write (iout,'(i5,f10.5)') (i,sc_parmin_nucl(j,i),j=1,9) + enddo + endif + ! ! Read the parameters of the probability distribution/energy expression ! of the side chains. @@ -1595,6 +1717,48 @@ enddo endif #endif + allocate(itortyp_nucl(ntyp1_molec(2))) !(-ntyp1:ntyp1) + read (itorp_nucl,*,end=113,err=113) ntortyp_nucl +! print *,"ntortyp_nucl",ntortyp_nucl,ntyp_molec(2) +!el from energy module--------- + allocate(nterm_nucl(ntortyp_nucl,ntortyp_nucl)) !(-maxtor:maxtor,-maxtor:maxtor,2) + allocate(nlor_nucl(ntortyp_nucl,ntortyp_nucl)) !(-maxtor:maxtor,-maxtor:maxtor,2) + + allocate(vlor1_nucl(maxlor,ntortyp_nucl,ntortyp_nucl)) !(maxlor,-maxtor:maxtor,-maxtor:maxtor) + allocate(vlor2_nucl(maxlor,ntortyp_nucl,ntortyp_nucl)) + allocate(vlor3_nucl(maxlor,ntortyp_nucl,ntortyp_nucl)) !(maxlor,maxtor,maxtor) + allocate(v0_nucl(ntortyp_nucl,ntortyp_nucl)) !(-maxtor:maxtor,-maxtor:maxtor,2) + + allocate(v1_nucl(maxterm,ntortyp_nucl,ntortyp_nucl)) + allocate(v2_nucl(maxterm,ntortyp_nucl,ntortyp_nucl)) !(maxterm,-maxtor:maxtor,-maxtor:maxtor,2) +!el--------------------------- + nterm_nucl(:,:)=0 + nlor_nucl(:,:)=0 +!el-------------------- + read (itorp_nucl,*,end=113,err=113) & + (itortyp_nucl(i),i=1,ntyp_molec(2)) +! print *,itortyp_nucl(:) +!c write (iout,*) 'ntortyp',ntortyp + do i=1,ntortyp_nucl + do j=1,ntortyp_nucl + read (itorp_nucl,*,end=113,err=113) nterm_nucl(i,j),nlor_nucl(i,j) +! print *,nterm_nucl(i,j),nlor_nucl(i,j) + v0ij=0.0d0 + si=-1.0d0 + do k=1,nterm_nucl(i,j) + read (itorp_nucl,*,end=113,err=113) kk,v1_nucl(k,i,j),v2_nucl(k,i,j) + v0ij=v0ij+si*v1_nucl(k,i,j) + si=-si + enddo + do k=1,nlor_nucl(i,j) + read (itorp,*,end=113,err=113) kk,vlor1_nucl(k,i,j),& + vlor2_nucl(k,i,j),vlor3_nucl(k,i,j) + v0ij=v0ij+vlor1_nucl(k,i,j)/(1+vlor3_nucl(k,i,j)**2) + enddo + v0_nucl(i,j)=v0ij + enddo + enddo + ! Read of Side-chain backbone correlation parameters ! Modified 11 May 2012 by Adasko !CC @@ -1738,6 +1902,7 @@ #endif if (lprint) then + l=3 write (iout,'(/a/)') 'Torsional constants:' do i=1,nsccortyp do j=1,nsccortyp @@ -1782,88 +1947,88 @@ do i=0,nloctyp-1 read (ifourier,*,end=115,err=115) - read (ifourier,*,end=115,err=115) (b(ii),ii=1,13) + read (ifourier,*,end=115,err=115) (buse(ii),ii=1,13) if (lprint) then write (iout,*) 'Type',i - write (iout,'(a,i2,a,f10.5)') ('b(',ii,')=',b(ii),ii=1,13) + write (iout,'(a,i2,a,f10.5)') ('buse(',ii,')=',buse(ii),ii=1,13) endif - B1(1,i) = b(3) - B1(2,i) = b(5) - B1(1,-i) = b(3) - B1(2,-i) = -b(5) -! b1(1,i)=0.0d0 -! b1(2,i)=0.0d0 - B1tilde(1,i) = b(3) - B1tilde(2,i) =-b(5) - B1tilde(1,-i) =-b(3) - B1tilde(2,-i) =b(5) -! b1tilde(1,i)=0.0d0 -! b1tilde(2,i)=0.0d0 - B2(1,i) = b(2) - B2(2,i) = b(4) - B2(1,-i) =b(2) - B2(2,-i) =-b(4) - -! b2(1,i)=0.0d0 -! b2(2,i)=0.0d0 - CC(1,1,i)= b(7) - CC(2,2,i)=-b(7) - CC(2,1,i)= b(9) - CC(1,2,i)= b(9) - CC(1,1,-i)= b(7) - CC(2,2,-i)=-b(7) - CC(2,1,-i)=-b(9) - CC(1,2,-i)=-b(9) + B1(1,i) = buse(3) + B1(2,i) = buse(5) + B1(1,-i) = buse(3) + B1(2,-i) = -buse(5) +! buse1(1,i)=0.0d0 +! buse1(2,i)=0.0d0 + B1tilde(1,i) = buse(3) + B1tilde(2,i) =-buse(5) + B1tilde(1,-i) =-buse(3) + B1tilde(2,-i) =buse(5) +! buse1tilde(1,i)=0.0d0 +! buse1tilde(2,i)=0.0d0 + B2(1,i) = buse(2) + B2(2,i) = buse(4) + B2(1,-i) =buse(2) + B2(2,-i) =-buse(4) + +! buse2(1,i)=0.0d0 +! buse2(2,i)=0.0d0 + CC(1,1,i)= buse(7) + CC(2,2,i)=-buse(7) + CC(2,1,i)= buse(9) + CC(1,2,i)= buse(9) + CC(1,1,-i)= buse(7) + CC(2,2,-i)=-buse(7) + CC(2,1,-i)=-buse(9) + CC(1,2,-i)=-buse(9) ! CC(1,1,i)=0.0d0 ! CC(2,2,i)=0.0d0 ! CC(2,1,i)=0.0d0 ! CC(1,2,i)=0.0d0 - Ctilde(1,1,i)=b(7) - Ctilde(1,2,i)=b(9) - Ctilde(2,1,i)=-b(9) - Ctilde(2,2,i)=b(7) - Ctilde(1,1,-i)=b(7) - Ctilde(1,2,-i)=-b(9) - Ctilde(2,1,-i)=b(9) - Ctilde(2,2,-i)=b(7) + Ctilde(1,1,i)=buse(7) + Ctilde(1,2,i)=buse(9) + Ctilde(2,1,i)=-buse(9) + Ctilde(2,2,i)=buse(7) + Ctilde(1,1,-i)=buse(7) + Ctilde(1,2,-i)=-buse(9) + Ctilde(2,1,-i)=buse(9) + Ctilde(2,2,-i)=buse(7) ! Ctilde(1,1,i)=0.0d0 ! Ctilde(1,2,i)=0.0d0 ! Ctilde(2,1,i)=0.0d0 ! Ctilde(2,2,i)=0.0d0 - DD(1,1,i)= b(6) - DD(2,2,i)=-b(6) - DD(2,1,i)= b(8) - DD(1,2,i)= b(8) - DD(1,1,-i)= b(6) - DD(2,2,-i)=-b(6) - DD(2,1,-i)=-b(8) - DD(1,2,-i)=-b(8) + DD(1,1,i)= buse(6) + DD(2,2,i)=-buse(6) + DD(2,1,i)= buse(8) + DD(1,2,i)= buse(8) + DD(1,1,-i)= buse(6) + DD(2,2,-i)=-buse(6) + DD(2,1,-i)=-buse(8) + DD(1,2,-i)=-buse(8) ! DD(1,1,i)=0.0d0 ! DD(2,2,i)=0.0d0 ! DD(2,1,i)=0.0d0 ! DD(1,2,i)=0.0d0 - Dtilde(1,1,i)=b(6) - Dtilde(1,2,i)=b(8) - Dtilde(2,1,i)=-b(8) - Dtilde(2,2,i)=b(6) - Dtilde(1,1,-i)=b(6) - Dtilde(1,2,-i)=-b(8) - Dtilde(2,1,-i)=b(8) - Dtilde(2,2,-i)=b(6) + Dtilde(1,1,i)=buse(6) + Dtilde(1,2,i)=buse(8) + Dtilde(2,1,i)=-buse(8) + Dtilde(2,2,i)=buse(6) + Dtilde(1,1,-i)=buse(6) + Dtilde(1,2,-i)=-buse(8) + Dtilde(2,1,-i)=buse(8) + Dtilde(2,2,-i)=buse(6) ! Dtilde(1,1,i)=0.0d0 ! Dtilde(1,2,i)=0.0d0 ! Dtilde(2,1,i)=0.0d0 ! Dtilde(2,2,i)=0.0d0 - EE(1,1,i)= b(10)+b(11) - EE(2,2,i)=-b(10)+b(11) - EE(2,1,i)= b(12)-b(13) - EE(1,2,i)= b(12)+b(13) - EE(1,1,-i)= b(10)+b(11) - EE(2,2,-i)=-b(10)+b(11) - EE(2,1,-i)=-b(12)+b(13) - EE(1,2,-i)=-b(12)-b(13) + EE(1,1,i)= buse(10)+buse(11) + EE(2,2,i)=-buse(10)+buse(11) + EE(2,1,i)= buse(12)-buse(13) + EE(1,2,i)= buse(12)+buse(13) + EE(1,1,-i)= buse(10)+buse(11) + EE(2,2,-i)=-buse(10)+buse(11) + EE(2,1,-i)=-buse(12)+buse(13) + EE(1,2,-i)=-buse(12)-buse(13) ! ee(1,1,i)=1.0d0 ! ee(2,2,i)=1.0d0 @@ -1927,6 +2092,7 @@ allocate(eps(ntyp,ntyp),sigmaii(ntyp,ntyp),rs0(ntyp,ntyp)) !(ntyp,ntyp) allocate(augm(ntyp,ntyp)) !(ntyp,ntyp) allocate(eps_scp(ntyp,2),rscp(ntyp,2)) !(ntyp,2) + allocate(sigma0(ntyp),rr0(ntyp),sigii(ntyp)) !(ntyp) allocate(chip(ntyp1),alp(ntyp1)) !(ntyp) allocate(epslip(ntyp,ntyp)) @@ -1965,7 +2131,7 @@ call printmat(ntyp,ntyp,ntyp,iout,restyp,eps) write (iout,'(/a)') 'One-body parameters:' write (iout,'(a,4x,a)') 'residue','sigma' - write (iout,'(a3,6x,f10.5)') (restyp(i),sigma0(i),i=1,ntyp) + write (iout,'(a3,6x,f10.5)') (restyp(i,1),sigma0(i),i=1,ntyp) endif ! goto 50 !----------------------- LJK potential -------------------------------- @@ -1979,7 +2145,7 @@ call printmat(ntyp,ntyp,ntyp,iout,restyp,eps) write (iout,'(/a)') 'One-body parameters:' write (iout,'(a,4x,2a)') 'residue',' sigma ',' r0 ' - write (iout,'(a3,6x,2f10.5)') (restyp(i),sigma0(i),rr0(i),& + write (iout,'(a3,6x,2f10.5)') (restyp(i,1),sigma0(i),rr0(i),& i=1,ntyp) endif ! goto 50 @@ -2010,7 +2176,7 @@ write (iout,'(/a)') 'One-body parameters:' write (iout,'(a,4x,4a)') 'residue',' sigma ','s||/s_|_^2',& ' chip ',' alph ' - write (iout,'(a3,6x,4f10.5)') (restyp(i),sigma0(i),sigii(i),& + write (iout,'(a3,6x,4f10.5)') (restyp(i,1),sigma0(i),sigii(i),& chip(i),alp(i),i=1,ntyp) endif ! goto 50 @@ -2027,7 +2193,7 @@ write (iout,'(/a)') 'One-body parameters:' write (iout,'(a,4x,5a)') 'residue',' sigma ',' r0 ',& 's||/s_|_^2',' chip ',' alph ' - write (iout,'(a3,6x,5f10.5)') (restyp(i),sigma0(i),rr0(i),& + write (iout,'(a3,6x,5f10.5)') (restyp(i,1),sigma0(i),rr0(i),& sigii(i),chip(i),alp(i),i=1,ntyp) endif case default @@ -2036,6 +2202,7 @@ end select continue close (isidep) + !----------------------------------------------------------------------- ! Calculate the "working" parameters of SC interactions. @@ -2139,11 +2306,90 @@ endif if (lprint) then write (iout,'(2(a3,2x),3(1pe10.3),5(0pf8.3))') & - restyp(i),restyp(j),aa_aq(i,j),bb_aq(i,j),augm(i,j),& + restyp(i,1),restyp(j,1),aa_aq(i,j),bb_aq(i,j),augm(i,j),& sigma(i,j),r0(i,j),chi(i,j),chi(j,i) endif enddo enddo + + allocate(eps_nucl(ntyp_molec(2),ntyp_molec(2))) + allocate(sigma_nucl(ntyp_molec(2),ntyp_molec(2))) !(ntyp_molec(2),ntyp_molec(2)) + allocate(elpp6_nucl(ntyp_molec(2),ntyp_molec(2))) !(ntyp_molec(2),ntyp_molec(2)) + allocate(elpp3_nucl(ntyp_molec(2),ntyp_molec(2))) !(ntyp,2) + allocate(elpp63_nucl(ntyp_molec(2),ntyp_molec(2))) !(ntyp_molec(2),ntyp_molec(2)) + allocate(elpp32_nucl(ntyp_molec(2),ntyp_molec(2))) !(ntyp,2) + allocate(chi_nucl(ntyp_molec(2),ntyp_molec(2)),chip_nucl(ntyp_molec(2),ntyp_molec(2))) !(ntyp_molec(2),ntyp_molec(2)) + allocate(ael3_nucl(ntyp_molec(2),ntyp_molec(2))) !(ntyp,2) + allocate(ael6_nucl(ntyp_molec(2),ntyp_molec(2))) !(ntyp,2) + allocate(ael32_nucl(ntyp_molec(2),ntyp_molec(2))) !(ntyp,2) + allocate(ael63_nucl(ntyp_molec(2),ntyp_molec(2))) !(ntyp,2) + allocate(aa_nucl(ntyp_molec(2),ntyp_molec(2))) !(ntyp,2) + allocate(bb_nucl(ntyp_molec(2),ntyp_molec(2))) !(ntyp,2) + allocate(r0_nucl(ntyp_molec(2),ntyp_molec(2))) !(ntyp,2) + allocate(sigmaii_nucl(ntyp_molec(2),ntyp_molec(2))) !(ntyp_molec(2),ntyp_molec(2)) + allocate(eps_scp_nucl(ntyp_molec(2)),rscp_nucl(ntyp_molec(2))) !(ntyp,2) + +! augm(:,:)=0.0D0 +! chip(:)=0.0D0 +! alp(:)=0.0D0 +! sigma0(:)=0.0D0 +! sigii(:)=0.0D0 +! rr0(:)=0.0D0 + + read (isidep_nucl,*) ipot_nucl +! print *,"TU?!",ipot_nucl + if (ipot_nucl.eq.1) then + do i=1,ntyp_molec(2) + do j=i,ntyp_molec(2) + read (isidep_nucl,*) eps_nucl(i,j),sigma_nucl(i,j),elpp6_nucl(i,j),& + elpp3_nucl(i,j), elpp63_nucl(i,j),elpp32_nucl(i,j) + enddo + enddo + else + do i=1,ntyp_molec(2) + do j=i,ntyp_molec(2) + read (isidep_nucl,*) eps_nucl(i,j),sigma_nucl(i,j),chi_nucl(i,j),& + chi_nucl(j,i),chip_nucl(i,j),chip_nucl(j,i),& + elpp6_nucl(i,j),elpp3_nucl(i,j),elpp63_nucl(i,j),elpp32_nucl(i,j) + enddo + enddo + endif +! rpp(1,1)=2**(1.0/6.0)*5.16158 + do i=1,ntyp_molec(2) + do j=i,ntyp_molec(2) + rrij=sigma_nucl(i,j) + r0_nucl(i,j)=rrij + r0_nucl(j,i)=rrij + rrij=rrij**expon + epsij=4*eps_nucl(i,j) + sigeps=dsign(1.0D0,epsij) + epsij=dabs(epsij) + aa_nucl(i,j)=epsij*rrij*rrij + bb_nucl(i,j)=-sigeps*epsij*rrij + ael3_nucl(i,j)=elpp3_nucl(i,j)*dsqrt(rrij) + ael6_nucl(i,j)=elpp6_nucl(i,j)*rrij + ael63_nucl(i,j)=elpp63_nucl(i,j)*rrij + ael32_nucl(i,j)=elpp32_nucl(i,j)*rrij + sigmaii_nucl(i,j)=sigma_nucl(i,j)/sqrt(1-(chi_nucl(i,j)+chi_nucl(j,i)- & + 2*chi_nucl(i,j)*chi_nucl(j,i))/(1-chi_nucl(i,j)*chi_nucl(j,i))) + enddo + do j=1,i-1 + aa_nucl(i,j)=aa_nucl(j,i) + bb_nucl(i,j)=bb_nucl(j,i) + ael3_nucl(i,j)=ael3_nucl(j,i) + ael6_nucl(i,j)=ael6_nucl(j,i) + ael63_nucl(i,j)=ael63_nucl(j,i) + ael32_nucl(i,j)=ael32_nucl(j,i) + elpp3_nucl(i,j)=elpp3_nucl(j,i) + elpp6_nucl(i,j)=elpp6_nucl(j,i) + elpp63_nucl(i,j)=elpp63_nucl(j,i) + elpp32_nucl(i,j)=elpp32_nucl(j,i) + eps_nucl(i,j)=eps_nucl(j,i) + sigma_nucl(i,j)=sigma_nucl(j,i) + sigmaii_nucl(i,j)=sigmaii_nucl(j,i) + enddo + enddo + write(iout,*) "tube param" read(itube,*) epspeptube,sigmapeptube,acavtubpep,bcavtubpep, & ccavtubpep,dcavtubpep,tubetranenepep @@ -2163,6 +2409,174 @@ sc_bb_tube_par(i)=-sigeps*4.0d0*epssctube*sigmasctube write(iout,*) sc_aa_tube_par(i), sc_bb_tube_par(i),tubetranene(i) enddo +!-----------------READING SC BASE POTENTIALS----------------------------- + allocate(eps_scbase(ntyp_molec(1),ntyp_molec(2))) + allocate(sigma_scbase(ntyp_molec(1),ntyp_molec(2))) + allocate(chi_scbase(ntyp_molec(1),ntyp_molec(2),2)) + allocate(chipp_scbase(ntyp_molec(1),ntyp_molec(2),2)) + allocate(alphasur_scbase(4,ntyp_molec(1),ntyp_molec(2))) + allocate(sigmap1_scbase(ntyp_molec(1),ntyp_molec(2))) + allocate(sigmap2_scbase(ntyp_molec(1),ntyp_molec(2))) + allocate(chis_scbase(ntyp_molec(1),ntyp_molec(2),2)) + allocate(dhead_scbasei(ntyp_molec(1),ntyp_molec(2))) + allocate(dhead_scbasej(ntyp_molec(1),ntyp_molec(2))) + allocate(rborn_scbasei(ntyp_molec(1),ntyp_molec(2))) + allocate(rborn_scbasej(ntyp_molec(1),ntyp_molec(2))) + allocate(wdipdip_scbase(3,ntyp_molec(1),ntyp_molec(2))) + allocate(wqdip_scbase(2,ntyp_molec(1),ntyp_molec(2))) + allocate(alphapol_scbase(ntyp_molec(1),ntyp_molec(2))) + allocate(epsintab_scbase(ntyp_molec(1),ntyp_molec(2))) + + + do i=1,ntyp_molec(1) + do j=1,ntyp_molec(2)-1 ! without U then we will take T for U + write (*,*) "Im in ", i, " ", j + read(isidep_scbase,*) & + eps_scbase(i,j),sigma_scbase(i,j),chi_scbase(i,j,1),& + chi_scbase(i,j,2),chipp_scbase(i,j,1),chipp_scbase(i,j,2) + write(*,*) "eps",eps_scbase(i,j) + read(isidep_scbase,*) & + (alphasur_scbase(k,i,j),k=1,4),sigmap1_scbase(i,j),sigmap2_scbase(i,j), & + chis_scbase(i,j,1),chis_scbase(i,j,2) + read(isidep_scbase,*) & + dhead_scbasei(i,j), & + dhead_scbasej(i,j), & + rborn_scbasei(i,j),rborn_scbasej(i,j) + read(isidep_scbase,*) & + (wdipdip_scbase(k,i,j),k=1,3), & + (wqdip_scbase(k,i,j),k=1,2) + read(isidep_scbase,*) & + alphapol_scbase(i,j), & + epsintab_scbase(i,j) + END DO + END DO + allocate(aa_scbase(ntyp_molec(1),ntyp_molec(2))) + allocate(bb_scbase(ntyp_molec(1),ntyp_molec(2))) + + do i=1,ntyp_molec(1) + do j=1,ntyp_molec(2)-1 + epsij=eps_scbase(i,j) + rrij=sigma_scbase(i,j) +! r0(i,j)=rrij +! r0(j,i)=rrij + rrij=rrij**expon +! epsij=eps(i,j) + sigeps=dsign(1.0D0,epsij) + epsij=dabs(epsij) + aa_scbase(i,j)=epsij*rrij*rrij + bb_scbase(i,j)=-sigeps*epsij*rrij + enddo + enddo +!-----------------READING PEP BASE POTENTIALS------------------- + allocate(eps_pepbase(ntyp_molec(2))) + allocate(sigma_pepbase(ntyp_molec(2))) + allocate(chi_pepbase(ntyp_molec(2),2)) + allocate(chipp_pepbase(ntyp_molec(2),2)) + allocate(alphasur_pepbase(4,ntyp_molec(2))) + allocate(sigmap1_pepbase(ntyp_molec(2))) + allocate(sigmap2_pepbase(ntyp_molec(2))) + allocate(chis_pepbase(ntyp_molec(2),2)) + allocate(wdipdip_pepbase(3,ntyp_molec(2))) + + + do j=1,ntyp_molec(2)-1 ! without U then we will take T for U + write (*,*) "Im in ", i, " ", j + read(isidep_pepbase,*) & + eps_pepbase(j),sigma_pepbase(j),chi_pepbase(j,1),& + chi_pepbase(j,2),chipp_pepbase(j,1),chipp_pepbase(j,2) + write(*,*) "eps",eps_pepbase(j) + read(isidep_pepbase,*) & + (alphasur_pepbase(k,j),k=1,4),sigmap1_pepbase(j),sigmap2_pepbase(j), & + chis_pepbase(j,1),chis_pepbase(j,2) + read(isidep_pepbase,*) & + (wdipdip_pepbase(k,j),k=1,3) + END DO + allocate(aa_pepbase(ntyp_molec(2))) + allocate(bb_pepbase(ntyp_molec(2))) + + do j=1,ntyp_molec(2)-1 + epsij=eps_pepbase(j) + rrij=sigma_pepbase(j) +! r0(i,j)=rrij +! r0(j,i)=rrij + rrij=rrij**expon +! epsij=eps(i,j) + sigeps=dsign(1.0D0,epsij) + epsij=dabs(epsij) + aa_pepbase(j)=epsij*rrij*rrij + bb_pepbase(j)=-sigeps*epsij*rrij + enddo +!--------------READING SC PHOSPHATE------------------------------------- + allocate(eps_scpho(ntyp_molec(1))) + allocate(sigma_scpho(ntyp_molec(1))) + allocate(chi_scpho(ntyp_molec(1),2)) + allocate(chipp_scpho(ntyp_molec(1),2)) + allocate(alphasur_scpho(4,ntyp_molec(1))) + allocate(sigmap1_scpho(ntyp_molec(1))) + allocate(sigmap2_scpho(ntyp_molec(1))) + allocate(chis_scpho(ntyp_molec(1),2)) + allocate(wqq_scpho(ntyp_molec(1))) + allocate(wqdip_scpho(2,ntyp_molec(1))) + allocate(alphapol_scpho(ntyp_molec(1))) + allocate(epsintab_scpho(ntyp_molec(1))) + allocate(dhead_scphoi(ntyp_molec(1))) + allocate(rborn_scphoi(ntyp_molec(1))) + allocate(rborn_scphoj(ntyp_molec(1))) + allocate(alphi_scpho(ntyp_molec(1))) + + +! j=1 + do j=1,ntyp_molec(1) ! without U then we will take T for U + write (*,*) "Im in scpho ", i, " ", j + read(isidep_scpho,*) & + eps_scpho(j),sigma_scpho(j),chi_scpho(j,1),& + chi_scpho(j,2),chipp_scpho(j,1),chipp_scpho(j,2) + write(*,*) "eps",eps_scpho(j) + read(isidep_scpho,*) & + (alphasur_scpho(k,j),k=1,4),sigmap1_scpho(j),sigmap2_scpho(j), & + chis_scpho(j,1),chis_scpho(j,2) + read(isidep_scpho,*) & + (wqdip_scpho(k,j),k=1,2),wqq_scpho(j),dhead_scphoi(j) + read(isidep_scpho,*) & + epsintab_scpho(j),alphapol_scpho(j),rborn_scphoi(j),rborn_scphoj(j), & + alphi_scpho(j) + + END DO + allocate(aa_scpho(ntyp_molec(1))) + allocate(bb_scpho(ntyp_molec(1))) + + do j=1,ntyp_molec(1) + epsij=eps_scpho(j) + rrij=sigma_scpho(j) +! r0(i,j)=rrij +! r0(j,i)=rrij + rrij=rrij**expon +! epsij=eps(i,j) + sigeps=dsign(1.0D0,epsij) + epsij=dabs(epsij) + aa_scpho(j)=epsij*rrij*rrij + bb_scpho(j)=-sigeps*epsij*rrij + enddo + + + read(isidep_peppho,*) & + eps_peppho,sigma_peppho + read(isidep_peppho,*) & + (alphasur_peppho(k),k=1,4),sigmap1_peppho,sigmap2_peppho + read(isidep_peppho,*) & + (wqdip_peppho(k),k=1,2) + + epsij=eps_peppho + rrij=sigma_peppho +! r0(i,j)=rrij +! r0(j,i)=rrij + rrij=rrij**expon +! epsij=eps(i,j) + sigeps=dsign(1.0D0,epsij) + epsij=dabs(epsij) + aa_peppho=epsij*rrij*rrij + bb_peppho=-sigeps*epsij*rrij + allocate(aad(ntyp,2),bad(ntyp,2)) !(ntyp,2) bad(:,:)=0.0D0 @@ -2216,6 +2630,20 @@ endif ! lprint=.false. #endif + allocate(aad_nucl(ntyp_molec(2)),bad_nucl(ntyp_molec(2))) !(ntyp,2) + + do i=1,ntyp_molec(2) + read (iscpp_nucl,*,end=118,err=118) eps_scp_nucl(i),rscp_nucl(i) + enddo + do i=1,ntyp_molec(2) + aad_nucl(i)=dabs(eps_scp_nucl(i))*rscp_nucl(i)**12 + bad_nucl(i)=-2*eps_scp_nucl(i)*rscp_nucl(i)**6 + enddo + r0pp=1.12246204830937298142*5.16158 + epspp=4.95713/4 + AEES=108.661 + BEES=0.433246 + ! ! Define the constants of the disulfide bridge ! @@ -2310,11 +2738,11 @@ ! Read the PDB file and convert the peptide geometry into virtual-chain ! geometry. use geometry_data - use energy_data, only: itype + use energy_data, only: itype,istype use control_data use compare_data use MPI_data - use control, only: rescode + use control, only: rescode,sugarcode ! implicit real*8 (a-h,o-z) ! include 'DIMENSIONS' ! include 'COMMON.LOCAL' @@ -2327,7 +2755,7 @@ ! include 'COMMON.CONTROL' ! include 'COMMON.DISTFIT' ! include 'COMMON.SETUP' - integer :: i,j,ibeg,ishift1,ires,iii,ires_old,ishift!,ity!,& + integer :: i,j,ibeg,ishift1,ires,iii,ires_old,ishift,k!,ity!,& ! ishift_pdb logical :: lprn=.true.,fail real(kind=8),dimension(3) :: e1,e2,e3 @@ -2336,29 +2764,48 @@ character(len=5) :: atom character(len=80) :: card real(kind=8),dimension(3,20) :: sccor - integer :: kkk,lll,icha,kupa !rescode, + integer :: kkk,lll,icha,kupa,molecule,counter,seqalingbegin !rescode, + integer :: isugar,molecprev,firstion + character*1 :: sugar real(kind=8) :: cou + real(kind=8),dimension(3) :: ccc !el local varables integer,dimension(2,maxres/3) :: hfrag_alloc integer,dimension(4,maxres/3) :: bfrag_alloc real(kind=8),dimension(3,maxres2+2,maxperm) :: cref_alloc !(3,maxres2+2,maxperm) - + real(kind=8),dimension(:,:), allocatable :: c_temporary + integer,dimension(:,:) , allocatable :: itype_temporary + integer,dimension(:),allocatable :: istype_temp efree_temp=0.0d0 ibeg=1 ishift1=0 ishift=0 + molecule=1 + counter=0 ! write (2,*) "UNRES_PDB",unres_pdb ires=0 ires_old=0 +#ifdef WHAM_RUN + do i=1,nres + do j=1,5 + itype(i,j)=0 + enddo + enddo +#endif nres=0 iii=0 lsecondary=.false. nhfrag=0 nbfrag=0 + do j=1,5 + nres_molec(j)=0 + enddo + + !----------------------------- allocate(hfrag(2,maxres/3)) !(2,maxres/3) allocate(bfrag(4,maxres/3)) !(4,maxres/3) - + if(.not. allocated(istype)) allocate(istype(maxres)) do i=1,100000 read (ipdbin,'(a80)',end=10) card ! write (iout,'(a)') card @@ -2384,9 +2831,11 @@ else if (card(:3).eq.'TER') then ! End current chain ires_old=ires+2 + ishift=ishift+1 ishift1=ishift1+1 - itype(ires_old,1)=ntyp1 - itype(ires_old-1,1)=ntyp1 + itype(ires_old,molecule)=ntyp1_molec(molecule) + itype(ires_old-1,molecule)=ntyp1_molec(molecule) + nres_molec(molecule)=nres_molec(molecule)+2 ibeg=2 ! write (iout,*) "Chain ended",ires,ishift,ires_old if (unres_pdb) then @@ -2402,6 +2851,7 @@ ! Read free energy if (index(card,"FREE ENERGY").gt.0) read(card(35:),*) efree_temp ! Fish out the ATOM cards. +! write(iout,*) 'card',card(1:20) if (index(card(1:4),'ATOM').gt.0) then read (card(12:16),*) atom ! write (iout,*) "! ",atom," !",ires @@ -2436,6 +2886,7 @@ if (res.ne.'GLY' .and. res.ne. 'ACE') then ishift=ishift-1 itype(1,1)=ntyp1 + nres_molec(molecule)=nres_molec(molecule)+1 endif ires=ires-ishift+ishift1 ires_old=ires @@ -2448,17 +2899,37 @@ ishift1=ishift1-1 !!!!! ! write (iout,*) "New chain started",ires,ishift,ishift1,"!" ires=ires-ishift+ishift1 +! print *,ires,ishift,ishift1 ires_old=ires ibeg=0 else ishift=ishift-(ires-ishift+ishift1-ires_old-1) ires=ires-ishift+ishift1 ires_old=ires - endif + endif +! print *,'atom',ires,atom if (res.eq.'ACE' .or. res.eq.'NHE') then itype(ires,1)=10 else - itype(ires,1)=rescode(ires,res,0) + if (atom.eq.'CA '.or.atom.eq.'N ') then + molecule=1 + itype(ires,molecule)=rescode(ires,res,0,molecule) + firstion=0 +! nres_molec(molecule)=nres_molec(molecule)+1 + else + molecule=2 + itype(ires,molecule)=rescode(ires,res(2:3),0,molecule) +! nres_molec(molecule)=nres_molec(molecule)+1 + read (card(19:19),'(a1)') sugar + isugar=sugarcode(sugar,ires) +! if (ibeg.eq.1) then +! istype(1)=isugar +! else + istype(ires)=isugar +! print *,"ires=",ires,istype(ires) +! endif + + endif endif else ires=ires-ishift+ishift1 @@ -2471,31 +2942,123 @@ if (atom.eq.'CA' .or. atom.eq.'CH3' .or. & res.eq.'NHE'.and.atom(:2).eq.'HN') then read(card(31:54),'(3f8.3)') (c(j,ires),j=1,3) +! print *,ires,ishift,ishift1 ! write (iout,*) "backbone ",atom #ifdef DEBUG write (iout,'(2i3,2x,a,3f8.3)') & ires,itype(ires,1),res,(c(j,ires),j=1,3) #endif iii=iii+1 + nres_molec(molecule)=nres_molec(molecule)+1 do j=1,3 sccor(j,iii)=c(j,ires) enddo + else if (.not.unres_pdb .and. (atom.eq."C1'" .or. & + atom.eq."C2'" .or. atom.eq."C3'" & + .or. atom.eq."C4'" .or. atom.eq."O4'")) then + read(card(31:54),'(3f8.3)') (ccc(j),j=1,3) +!c write (2,'(i5,3f10.5)') ires,(ccc(j),j=1,3) +! print *,ires,ishift,ishift1 + counter=counter+1 +! iii=iii+1 +! do j=1,3 +! sccor(j,iii)=c(j,ires) +! enddo + do j=1,3 + c(j,ires)=c(j,ires)+ccc(j)/5.0 + enddo + print *,counter,molecule + if (counter.eq.5) then +! iii=iii+1 + nres_molec(molecule)=nres_molec(molecule)+1 + firstion=0 +! do j=1,3 +! sccor(j,iii)=c(j,ires) +! enddo + counter=0 + endif +! print *, "ATOM",atom(1:3) + else if (atom.eq."C5'") then + read (card(19:19),'(a1)') sugar + isugar=sugarcode(sugar,ires) + if (ibeg.eq.1) then + istype(1)=isugar + else + istype(ires)=isugar +! print *,ires,istype(ires) + endif + if (unres_pdb) then + molecule=2 +! print *,"nres_molec(molecule)",nres_molec(molecule),ires + read(card(31:54),'(3f8.3)') (c(j,ires),j=1,3) + nres_molec(molecule)=nres_molec(molecule)+1 + print *,"nres_molec(molecule)",nres_molec(molecule),ires + + else + iii=iii+1 + read(card(31:54),'(3f8.3)') (sccor(j,iii),j=1,3) + endif + else if ((atom.eq."C1'").and.unres_pdb) then + iii=iii+1 + read(card(31:54),'(3f8.3)') (sccor(j,iii),j=1,3) ! write (*,*) card(23:27),ires,itype(ires,1) else if (atom.ne.'O'.and.atom(1:1).ne.'H' .and. & atom.ne.'N' .and. atom.ne.'C' .and. & atom(:2).ne.'1H' .and. atom(:2).ne.'2H' .and. & - atom.ne.'OXT' .and. atom(:2).ne.'3H') then + atom.ne.'OXT' .and. atom(:2).ne.'3H' & + .and. atom.ne.'P '.and. & + atom(1:1).ne.'H' .and. & + atom.ne.'OP1' .and. atom.ne.'OP2 '.and. atom.ne.'OP3'& + ) then ! write (iout,*) "sidechain ",atom +! write (iout,*) "sidechain ",atom,molecule,ires,atom(3:3) + if ((molecule.ne.2).or.(atom(3:3).ne."'")) then +! write (iout,*) "sidechain ",atom,molecule,ires,atom(3:3) iii=iii+1 read(card(31:54),'(3f8.3)') (sccor(j,iii),j=1,3) + endif endif - endif + else if ((ions).and.(card(1:6).eq.'HETATM')) then + if (firstion.eq.0) then + firstion=1 + if (unres_pdb) then + do j=1,3 + dc(j,ires)=sccor(j,iii) + enddo + else + call sccenter(ires,iii,sccor) + endif + endif + read (card(12:16),*) atom + print *,"HETATOM", atom + read (card(18:20),'(a3)') res + if ((atom(1:2).eq.'NA').or.(atom(1:2).eq.'CL').or.& + (atom(1:2).eq.'CA').or.(atom(1:2).eq.'MG') & + .or.(atom(1:2).eq.'K ')) & + then + ires=ires+1 + if (molecule.ne.5) molecprev=molecule + molecule=5 + nres_molec(molecule)=nres_molec(molecule)+1 + print *,"HERE",nres_molec(molecule) + res=res(2:3)//' ' + itype(ires,molecule)=rescode(ires,res,0,molecule) + read(card(31:54),'(3f8.3)') (c(j,ires),j=1,3) + endif + endif !atom enddo 10 write (iout,'(a,i5)') ' Number of residues found: ',ires if (ires.eq.0) return ! Calculate dummy residue coordinates inside the "chain" of a multichain ! system nres=ires + if (((ires_old.ne.ires).and.(molecule.ne.5)) & + .and.(.not.unres_pdb)) & + nres_molec(molecule)=nres_molec(molecule)-2 + print *,'I have',nres, nres_molec(:) + + do k=1,4 ! ions are without dummy + if (nres_molec(k).eq.0) cycle do i=2,nres-1 ! write (iout,*) i,itype(i,1) ! if (itype(i,1).eq.ntyp1) then @@ -2506,56 +3069,70 @@ ! dc(j,i)=c(j,i) ! enddo ! endif - if (itype(i,1).eq.ntyp1) then - if (itype(i+1,1).eq.ntyp1) then + if (itype(i,k).eq.ntyp1_molec(k)) then + if (itype(i+1,k).eq.ntyp1_molec(k)) then + if (itype(i+2,k).eq.0) then +! print *,"masz sieczke" + do j=1,5 + if (itype(i+2,j).ne.0) then + itype(i+1,k)=0 + itype(i+1,j)=ntyp1_molec(j) + nres_molec(k)=nres_molec(k)-1 + nres_molec(j)=nres_molec(j)+1 + go to 3331 + endif + enddo + 3331 continue + endif ! 16/01/2014 by Adasko: Adding to dummy atoms in the chain ! first is connected prevous chain (itype(i+1,1).eq.ntyp1)=true ! second dummy atom is conected to next chain itype(i+1,1).eq.ntyp1=false - if (unres_pdb) then +! if (unres_pdb) then ! 2/15/2013 by Adam: corrected insertion of the last dummy residue ! print *,i,'tu dochodze' - call refsys(i-3,i-2,i-1,e1,e2,e3,fail) - if (fail) then - e2(1)=0.0d0 - e2(2)=1.0d0 - e2(3)=0.0d0 - endif !fail - print *,i,'a tu?' - do j=1,3 - c(j,i)=c(j,i-1)-1.9d0*e2(j) - enddo - else !unres_pdb +! call refsys(i-3,i-2,i-1,e1,e2,e3,fail) +! if (fail) then +! e2(1)=0.0d0 +! e2(2)=1.0d0 +! e2(3)=0.0d0 +! endif !fail +! print *,i,'a tu?' +! do j=1,3 +! c(j,i)=c(j,i-1)-1.9d0*e2(j) +! enddo +! else !unres_pdb do j=1,3 dcj=(c(j,i-2)-c(j,i-3))/2.0 if (dcj.eq.0) dcj=1.23591524223 c(j,i)=c(j,i-1)+dcj c(j,nres+i)=c(j,i) enddo - endif !unres_pdb +! endif !unres_pdb else !itype(i+1,1).eq.ntyp1 - if (unres_pdb) then +! if (unres_pdb) then ! 2/15/2013 by Adam: corrected insertion of the first dummy residue - call refsys(i+1,i+2,i+3,e1,e2,e3,fail) - if (fail) then - e2(1)=0.0d0 - e2(2)=1.0d0 - e2(3)=0.0d0 - endif +! call refsys(i+1,i+2,i+3,e1,e2,e3,fail) +! if (fail) then +! e2(1)=0.0d0 +! e2(2)=1.0d0 +! e2(3)=0.0d0 +! endif do j=1,3 c(j,i)=c(j,i+1)-1.9d0*e2(j) enddo - else !unres_pdb +! else !unres_pdb do j=1,3 dcj=(c(j,i+3)-c(j,i+2))/2.0 if (dcj.eq.0) dcj=1.23591524223 c(j,i)=c(j,i+1)-dcj c(j,nres+i)=c(j,i) enddo - endif !unres_pdb +! endif !unres_pdb endif !itype(i+1,1).eq.ntyp1 endif !itype.eq.ntyp1 enddo + enddo ! Calculate the CM of the last side chain. if (iii.gt.0) then if (unres_pdb) then @@ -2569,28 +3146,33 @@ ! nres=ires nsup=nres nstart_sup=1 - if (itype(nres,1).ne.10) then +! print *,"molecule",molecule + if ((itype(nres,1).ne.10)) then nres=nres+1 - itype(nres,1)=ntyp1 - if (unres_pdb) then + if (molecule.eq.5) molecule=molecprev + itype(nres,molecule)=ntyp1_molec(molecule) + nres_molec(molecule)=nres_molec(molecule)+1 +! if (unres_pdb) then ! 2/15/2013 by Adam: corrected insertion of the last dummy residue - call refsys(nres-3,nres-2,nres-1,e1,e2,e3,fail) - if (fail) then - e2(1)=0.0d0 - e2(2)=1.0d0 - e2(3)=0.0d0 - endif - do j=1,3 - c(j,nres)=c(j,nres-1)-1.9d0*e2(j) - enddo - else +! call refsys(nres-3,nres-2,nres-1,e1,e2,e3,fail) +! if (fail) then +! e2(1)=0.0d0 +! e2(2)=1.0d0 +! e2(3)=0.0d0 +! endif +! do j=1,3 +! c(j,nres)=c(j,nres-1)-1.9d0*e2(j) +! enddo +! else 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 +! endif endif +! print *,'I have',nres, nres_molec(:) + !el kontrola nres w pliku inputowym WHAM-a w porownaniu z wartoscia wczytana z pliku pdb #ifdef WHAM_RUN if (nres.ne.nres0) then @@ -2638,6 +3220,7 @@ c(j,nres+1)=c(j,1) c(j,2*nres)=c(j,nres) enddo + if (itype(1,1).eq.ntyp1) then nsup=nsup-1 nstart_sup=2 @@ -2660,6 +3243,24 @@ enddo endif endif +! First lets assign correct dummy to correct type of chain +! 1) First residue + if (itype(1,1).eq.ntyp1) then + if (itype(2,1).eq.0) then + do j=2,5 + if (itype(2,j).ne.0) then + itype(1,1)=0 + itype(1,j)=ntyp1_molec(j) + nres_molec(1)=nres_molec(1)-1 + nres_molec(j)=nres_molec(j)+1 + go to 3231 + endif + enddo +3231 continue + endif + endif + print *,'I have',nres, nres_molec(:) + ! Copy the coordinates to reference coordinates ! do i=1,2*nres ! do j=1,3 @@ -2673,8 +3274,8 @@ write (iout,'(a,3(3x,a5),5x,3(3x,a5))') & "Residue","X(CA)","Y(CA)","Z(CA)","X(SC)","Y(SC)","Z(SC)" do ires=1,nres - write (iout,'(a3,1x,i3,3f8.3,5x,3f8.3)') & - restyp(itype(ires,1)),ires,(c(j,ires),j=1,3),& + write (iout,'(5(a3,1x),i3,3f8.3,5x,3f8.3)') & + (restyp(itype(ires,j),j),j=1,5),ires,(c(j,ires),j=1,3),& (c(j,ires+nres),j=1,3) enddo endif @@ -2685,11 +3286,82 @@ "Backbone and SC coordinates as read from the PDB" do ires=1,nres write (iout,'(2i3,2x,a,3f8.3,5x,3f8.3)') & - ires,itype(ires,1),restyp(itype(ires,1)),(c(j,ires),j=1,3),& + ires,itype(ires,1),restyp(itype(ires,1),1),(c(j,ires),j=1,3),& (c(j,nres+ires),j=1,3) enddo endif +! NOW LETS ROCK! SORTING + allocate(c_temporary(3,2*nres)) + allocate(itype_temporary(nres,5)) + if (.not.allocated(molnum)) allocate(molnum(nres+1)) + if (.not.allocated(istype)) write(iout,*) & + "SOMETHING WRONG WITH ISTYTPE" + allocate(istype_temp(nres)) + itype_temporary(:,:)=0 + seqalingbegin=1 + do k=1,5 + do i=1,nres + if (itype(i,k).ne.0) then + do j=1,3 + c_temporary(j,seqalingbegin)=c(j,i) + c_temporary(j,seqalingbegin+nres)=c(j,i+nres) + enddo + itype_temporary(seqalingbegin,k)=itype(i,k) + print *,i,k,itype(i,k),itype_temporary(seqalingbegin,k),seqalingbegin + istype_temp(seqalingbegin)=istype(i) + molnum(seqalingbegin)=k + seqalingbegin=seqalingbegin+1 + endif + enddo + enddo + do i=1,2*nres + do j=1,3 + c(j,i)=c_temporary(j,i) + enddo + enddo + do k=1,5 + do i=1,nres + itype(i,k)=itype_temporary(i,k) + istype(i)=istype_temp(i) + enddo + enddo + if (itype(1,1).eq.ntyp1) then + nsup=nsup-1 + nstart_sup=2 + if (unres_pdb) then +! 2/15/2013 by Adam: corrected insertion of the first dummy residue + call refsys(2,3,4,e1,e2,e3,fail) + if (fail) then + e2(1)=0.0d0 + e2(2)=1.0d0 + e2(3)=0.0d0 + endif + do j=1,3 + c(j,1)=c(j,2)-1.9d0*e2(j) + enddo + else + 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 + endif + + if (lprn) then + write (iout,'(/a)') & + "Cartesian coordinates of the reference structure after sorting" + write (iout,'(a,3(3x,a5),5x,3(3x,a5))') & + "Residue","X(CA)","Y(CA)","Z(CA)","X(SC)","Y(SC)","Z(SC)" + do ires=1,nres + write (iout,'(5(a3,1x),i3,3f8.3,5x,3f8.3)') & + (restyp(itype(ires,j),j),j=1,5),ires,(c(j,ires),j=1,3),& + (c(j,ires+nres),j=1,3) + enddo + endif + +! print *,seqalingbegin,nres if(.not.allocated(vbld)) then allocate(vbld(2*nres)) do i=1,2*nres @@ -2768,6 +3440,7 @@ kkk=1 lll=0 cou=1 + write (iout,*) "symetr", symetr do i=1,nres lll=lll+1 !c write (iout,*) "spraw lancuchy",(c(j,i),j=1,3) @@ -2844,7 +3517,7 @@ do kkk=1,nperm write (iout,*) "nowa struktura", nperm do i=1,nres - write (iout,110) restyp(itype(i,1)),i,cref(1,i,kkk),& + write (iout,110) restyp(itype(i,1),1),i,cref(1,i,kkk),& cref(2,i,kkk),& cref(3,i,kkk),cref(1,nres+i,kkk),& cref(2,nres+i,kkk),cref(3,nres+i,kkk) @@ -2971,6 +3644,9 @@ write(iout,*) "shield_mode",shield_mode !C Varibles set size of box with_theta_constr = index(controlcard,"WITH_THETA_CONSTR").gt.0 + protein=index(controlcard,"PROTEIN").gt.0 + ions=index(controlcard,"IONS").gt.0 + nucleic=index(controlcard,"NUCLEIC").gt.0 write (iout,*) "with_theta_constr ",with_theta_constr AFMlog=(index(controlcard,'AFM')) selfguide=(index(controlcard,'SELFGUIDE')) @@ -3257,7 +3933,7 @@ ! character(len=80) :: ucase character(len=320) :: controlcard !el local variables - integer :: i + integer :: i,j real(kind=8) :: eta call card_concat(controlcard,.true.) @@ -3370,21 +4046,27 @@ if(me.eq.king.or..not.out1file) & write(iout,'(a60,f10.5)')"Eta of the solvent in natural units:",& eta - gamp=scal_fric*(pstok+rwat)*eta - stdfp=dsqrt(2*Rb*t_bath/d_time) - allocate(gamsc(ntyp1),stdfsc(ntyp1)) !(ntyp1) +! allocate(gamp + do j=1,5 !types of molecules + gamp(j)=scal_fric*(pstok(j)+rwat)*eta + stdfp(j)=dsqrt(2*Rb*t_bath/d_time) + enddo + allocate(gamsc(ntyp1,5),stdfsc(ntyp1,5)) !(ntyp1) + do j=1,5 !types of molecules do i=1,ntyp - gamsc(i)=scal_fric*(restok(i)+rwat)*eta - stdfsc(i)=dsqrt(2*Rb*t_bath/d_time) + gamsc(i,j)=scal_fric*(restok(i,j)+rwat)*eta + stdfsc(i,j)=dsqrt(2*Rb*t_bath/d_time) enddo + enddo + if(me.eq.king.or..not.out1file)then write (iout,'(/2a/)') & "Radii of site types and friction coefficients and std's of",& " stochastic forces of fully exposed sites" - write (iout,'(a5,f5.2,2f10.5)')'p',pstok,gamp,stdfp*dsqrt(gamp) + write (iout,'(a5,f5.2,2f10.5)')'p',pstok,gamp(1),stdfp*dsqrt(gamp(1)) do i=1,ntyp - write (iout,'(a5,f5.2,2f10.5)') restyp(i),restok(i),& - gamsc(i),stdfsc(i)*dsqrt(gamsc(i)) + write (iout,'(a5,f5.2,2f10.5)') restyp(i,1),restok(i,1),& + gamsc(i,1),stdfsc(i,1)*dsqrt(gamsc(i,1)) enddo endif else if (tbf) then @@ -3745,6 +4427,8 @@ ! Get parameter filenames and open the parameter files. call getenv_loc('BONDPAR',bondname) open (ibond,file=bondname,status='old',readonly,shared) + call getenv_loc('BONDPAR_NUCL',bondname_nucl) + open (ibond_nucl,file=bondname_nucl,status='old',readonly,shared) call getenv_loc('THETPAR',thetname) open (ithep,file=thetname,status='old',readonly,shared) call getenv_loc('ROTPAR',rotname) @@ -3759,6 +4443,19 @@ open (ielep,file=elename,status='old',readonly,shared) call getenv_loc('SIDEPAR',sidename) open (isidep,file=sidename,status='old',readonly,shared) + + call getenv_loc('THETPAR_NUCL',thetname_nucl) + open (ithep_nucl,file=thetname_nucl,status='old',readonly,shared) + call getenv_loc('ROTPAR_NUCL',rotname_nucl) + open (irotam_nucl,file=rotname_nucl,status='old',readonly,shared) + call getenv_loc('TORPAR_NUCL',torname_nucl) + open (itorp_nucl,file=torname_nucl,status='old',readonly,shared) + call getenv_loc('TORDPAR_NUCL',tordname_nucl) + open (itordp_nucl,file=tordname_nucl,status='old',readonly,shared) + call getenv_loc('SIDEPAR_NUCL',sidename_nucl) + open (isidep_nucl,file=sidename_nucl,status='old',readonly,shared) + + #elif (defined CRAY) || (defined AIX) open(1,file=pref_orig(:ilen(pref_orig))//'.inp',status='old',& action='read') @@ -3769,6 +4466,9 @@ ! Get parameter filenames and open the parameter files. call getenv_loc('BONDPAR',bondname) open (ibond,file=bondname,status='old',action='read') + call getenv_loc('BONDPAR_NUCL',bondname_nucl) + open (ibond_nucl,file=bondname_nucl,status='old',action='read') + ! print *,"Processor",myrank," opened file IBOND" call getenv_loc('THETPAR',thetname) open (ithep,file=thetname,status='old',action='read') @@ -3793,10 +4493,24 @@ ! print *,"Processor",myrank," opened file IELEP" call getenv_loc('SIDEPAR',sidename) open (isidep,file=sidename,status='old',action='read') + + call getenv_loc('THETPAR_NUCL',thetname_nucl) + open (ithep_nucl,file=thetname_nucl,status='old',action='read') + call getenv_loc('ROTPAR_NUCL',rotname_nucl) + open (irotam_nucl,file=rotname_nucl,status='old',action='read') + call getenv_loc('TORPAR_NUCL',torname_nucl) + open (itorp_nucl,file=torname_nucl,status='old',action='read') + call getenv_loc('TORDPAR_NUCL',tordname_nucl) + open (itordp_nucl,file=tordname_nucl,status='old',action='read') + call getenv_loc('SIDEPAR_NUCL',sidename_nucl) + open (isidep_nucl,file=sidename_nucl,status='old',action='read') + call getenv_loc('LIPTRANPAR',liptranname) open (iliptranpar,file=liptranname,status='old',action='read') call getenv_loc('TUBEPAR',tubename) open (itube,file=tubename,status='old',action='read') + call getenv_loc('IONPAR',ionname) + open (iion,file=ionname,status='old',action='read') ! print *,"Processor",myrank," opened file ISIDEP" ! print *,"Processor",myrank," opened parameter files" @@ -3807,6 +4521,9 @@ ! Get parameter filenames and open the parameter files. call getenv_loc('BONDPAR',bondname) open (ibond,file=bondname,status='old') + call getenv_loc('BONDPAR_NUCL',bondname_nucl) + open (ibond_nucl,file=bondname_nucl,status='old') + call getenv_loc('THETPAR',thetname) open (ithep,file=thetname,status='old') call getenv_loc('ROTPAR',rotname) @@ -3823,10 +4540,23 @@ open (ielep,file=elename,status='old') call getenv_loc('SIDEPAR',sidename) open (isidep,file=sidename,status='old') + + open (ithep_nucl,file=thetname_nucl,status='old') + call getenv_loc('ROTPAR_NUCL',rotname_nucl) + open (irotam_nucl,file=rotname_nucl,status='old') + call getenv_loc('TORPAR_NUCL',torname_nucl) + open (itorp_nucl,file=torname_nucl,status='old') + call getenv_loc('TORDPAR_NUCL',tordname_nucl) + open (itordp_nucl,file=tordname_nucl,status='old') + call getenv_loc('SIDEPAR_NUCL',sidename_nucl) + open (isidep_nucl,file=sidename_nucl,status='old') + call getenv_loc('LIPTRANPAR',liptranname) open (iliptranpar,file=liptranname,status='old') call getenv_loc('TUBEPAR',tubename) open (itube,file=tubename,status='old') + call getenv_loc('IONPAR',ionname) + open (iion,file=ionname,status='old') #else open(1,file=pref_orig(:ilen(pref_orig))//'.inp',status='old',& readonly) @@ -3835,6 +4565,8 @@ ! Get parameter filenames and open the parameter files. call getenv_loc('BONDPAR',bondname) open (ibond,file=bondname,status='old',action='read') + call getenv_loc('BONDPAR_NUCL',bondname_nucl) + open (ibond_nucl,file=bondname_nucl,status='old',action='read') call getenv_loc('THETPAR',thetname) open (ithep,file=thetname,status='old',action='read') call getenv_loc('ROTPAR',rotname) @@ -3857,16 +4589,50 @@ open (ielep,file=elename,status='old',readonly) call getenv_loc('SIDEPAR',sidename) open (isidep,file=sidename,status='old',readonly) + + call getenv_loc('THETPAR_NUCL',thetname_nucl) + open (ithep_nucl,file=thetname_nucl,status='old',action='read') + call getenv_loc('ROTPAR_NUCL',rotname_nucl) + open (irotam_nucl,file=rotname_nucl,status='old',action='read') + call getenv_loc('TORPAR_NUCL',torname_nucl) + open (itorp_nucl,file=torname_nucl,status='old',action='read') + call getenv_loc('TORDPAR_NUCL',tordname_nucl) + open (itordp_nucl,file=tordname_nucl,status='old',action='read') + call getenv_loc('SIDEPAR_NUCL',sidename_nucl) + open (isidep_nucl,file=sidename_nucl,status='old',action='read') + call getenv_loc('SIDEPAR_SCBASE',sidename_scbase) + open (isidep_scbase,file=sidename_scbase,status='old',action='read') + call getenv_loc('PEPPAR_PEPBASE',pepname_pepbase) + open (isidep_pepbase,file=pepname_pepbase,status='old',action='read') + call getenv_loc('SCPAR_PHOSPH',pepname_scpho) + open (isidep_scpho,file=pepname_scpho,status='old',action='read') + call getenv_loc('PEPPAR_PHOSPH',pepname_peppho) + open (isidep_peppho,file=pepname_peppho,status='old',action='read') + + call getenv_loc('LIPTRANPAR',liptranname) open (iliptranpar,file=liptranname,status='old',action='read') call getenv_loc('TUBEPAR',tubename) open (itube,file=tubename,status='old',action='read') + call getenv_loc('IONPAR',ionname) + open (iion,file=ionname,status='old',action='read') #ifndef CRYST_SC call getenv_loc('ROTPARPDB',rotname_pdb) open (irotam_pdb,file=rotname_pdb,status='old',action='read') #endif #endif + call getenv_loc('SCPPAR_NUCL',scpname_nucl) +#if defined(WINIFL) || defined(WINPGI) + open (iscpp_nucl,file=scpname_nucl,status='old',readonly,shared) +#elif (defined CRAY) || (defined AIX) + open (iscpp_nucl,file=scpname_nucl,status='old',action='read') +#elif (defined G77) + open (iscpp_nucl,file=scpname_nucl,status='old') +#else + open (iscpp_nucl,file=scpname_nucl,status='old',action='read') +#endif + #ifndef OLDSCP ! ! 8/9/01 In the newest version SCp interaction constants are read from a file