X-Git-Url: http://mmka.chem.univ.gda.pl/gitweb/?a=blobdiff_plain;f=source%2Funres%2Fsrc_MD%2Fparmread.F;h=2e953a2a26e2eea73dcfe85ffab100195e863504;hb=2958e81241cbcb0ccf96891c89c753689ac6f709;hp=b3f26b3a301995a8b9359529a22d14902d175b30;hpb=478a9d9a1c99eb3f4bc4ca676ff3162bdd01d633;p=unres.git diff --git a/source/unres/src_MD/parmread.F b/source/unres/src_MD/parmread.F index b3f26b3..2e953a2 100644 --- a/source/unres/src_MD/parmread.F +++ b/source/unres/src_MD/parmread.F @@ -276,6 +276,17 @@ C enddo call flush(iout) endif + write (2,*) "Start reading THETA_PDB" + do i=1,ntyp + read (ithep_pdb,*,err=111,end=111) a0thet(i),(athet(j,i),j=1,2), + & (bthet(j,i),j=1,2) + read (ithep_pdb,*,err=111,end=111) (polthet(j,i),j=0,3) + read (ithep_pdb,*,err=111,end=111) (gthet(j,i),j=1,3) + read (ithep_pdb,*,err=111,end=111) theta0(i),sig0(i),sigc0(i) + sigc0(i)=sigc0(i)**2 + enddo + write (2,*) "End reading THETA_PDB" + close (ithep_pdb) #endif close(ithep) #ifdef CRYST_SC @@ -301,10 +312,18 @@ C bsc(1,i)=0.0D0 read(irotam,*,end=112,err=112)(censc(k,1,i),k=1,3), & ((blower(k,l,1),l=1,k),k=1,3) + censc(1,1,-i)=censc(1,1,i) + censc(2,1,-i)=censc(2,1,i) + censc(3,1,-i)=-censc(3,1,i) + do j=2,nlob(i) read (irotam,*,end=112,err=112) bsc(j,i) read (irotam,*,end=112,err=112) (censc(k,j,i),k=1,3), & ((blower(k,l,j),l=1,k),k=1,3) + censc(1,j,-i)=censc(1,j,i) + censc(2,j,-i)=censc(2,j,i) + censc(3,j,-i)=-censc(3,j,i) +C BSC is amplitude of Gaussian enddo do j=1,nlob(i) do k=1,3 @@ -315,6 +334,14 @@ C enddo gaussc(k,l,j,i)=akl gaussc(l,k,j,i)=akl + if (((k.eq.3).and.(l.ne.3)) + & .or.((l.eq.3).and.(k.ne.3))) then + gaussc(k,l,j,-i)=-akl + gaussc(l,k,j,-i)=-akl + else + gaussc(k,l,j,-i)=akl + gaussc(l,k,j,-i)=akl + endif enddo enddo enddo @@ -363,6 +390,48 @@ C enddo endif enddo +C +C Read the parameters of the probability distribution/energy expression +C of the side chains. +C + do i=1,ntyp + read (irotam_pdb,'(3x,i3,f8.3)',end=112,err=112) nlob(i),dsc(i) + if (i.eq.10) then + dsc_inv(i)=0.0D0 + else + dsc_inv(i)=1.0D0/dsc(i) + endif + if (i.ne.10) then + do j=1,nlob(i) + do k=1,3 + do l=1,3 + blower(l,k,j)=0.0D0 + enddo + enddo + enddo + bsc(1,i)=0.0D0 + read(irotam_pdb,*,end=112,err=112)(censc(k,1,i),k=1,3), + & ((blower(k,l,1),l=1,k),k=1,3) + do j=2,nlob(i) + read (irotam_pdb,*,end=112,err=112) bsc(j,i) + read (irotam_pdb,*,end=112,err=112) (censc(k,j,i),k=1,3), + & ((blower(k,l,j),l=1,k),k=1,3) + enddo + do j=1,nlob(i) + do k=1,3 + do l=1,k + akl=0.0D0 + do m=1,3 + akl=akl+blower(k,m,j)*blower(l,m,j) + enddo + gaussc(k,l,j,i)=akl + gaussc(l,k,j,i)=akl + enddo + enddo + enddo + endif + enddo + close (irotam_pdb) #endif close(irotam) @@ -397,25 +466,38 @@ C Read torsional parameters C read (itorp,*,end=113,err=113) ntortyp read (itorp,*,end=113,err=113) (itortyp(i),i=1,ntyp) -c write (iout,*) 'ntortyp',ntortyp - do i=1,ntortyp - do j=1,ntortyp - read (itorp,*,end=113,err=113) nterm(i,j),nlor(i,j) + do iblock=1,2 + do i=-ntyp,-1 + itortyp(i)=-itortyp(-i) + enddo + write (iout,*) 'ntortyp',ntortyp + do i=0,ntortyp-1 + do j=-ntortyp+1,ntortyp-1 + read (itorp,*,end=113,err=113) nterm(i,j,iblock), + & nlor(i,j,iblock) + nterm(-i,-j,iblock)=nterm(i,j,iblock) + nlor(-i,-j,iblock)=nlor(i,j,iblock) v0ij=0.0d0 si=-1.0d0 - do k=1,nterm(i,j) - read (itorp,*,end=113,err=113) kk,v1(k,i,j),v2(k,i,j) - v0ij=v0ij+si*v1(k,i,j) + do k=1,nterm(i,j,iblock) + read (itorp,*,end=113,err=113) kk,v1(k,i,j,iblock), + & v2(k,i,j,iblock) + v1(k,-i,-j,iblock)=v1(k,i,j,iblock) + v2(k,-i,-j,iblock)=-v2(k,i,j,iblock) + v0ij=v0ij+si*v1(k,i,j,iblock) si=-si + write(iout,*) i,j,k,iblock,nterm(i,j,iblock),v1(k,-i,-j,iblock) enddo - do k=1,nlor(i,j) + do k=1,nlor(i,j,iblock) read (itorp,*,end=113,err=113) kk,vlor1(k,i,j), & vlor2(k,i,j),vlor3(k,i,j) v0ij=v0ij+vlor1(k,i,j)/(1+vlor3(k,i,j)**2) enddo - v0(i,j)=v0ij + v0(i,j,iblock)=v0ij + v0(-i,-j,iblock)=v0ij enddo enddo + enddo close (itorp) if (lprint) then write (iout,'(/a/)') 'Torsional constants:' @@ -423,11 +505,12 @@ c write (iout,*) 'ntortyp',ntortyp do j=1,ntortyp write (iout,*) 'ityp',i,' jtyp',j write (iout,*) 'Fourier constants' - do k=1,nterm(i,j) - write (iout,'(2(1pe15.5))') v1(k,i,j),v2(k,i,j) + do k=1,nterm(i,j,iblock) + write (iout,'(2(1pe15.5))') v1(k,i,j,iblock), + & v2(k,i,j,iblock) enddo write (iout,*) 'Lorenz constants' - do k=1,nlor(i,j) + do k=1,nlor(i,j,iblock) write (iout,'(3(1pe15.5))') & vlor1(k,i,j),vlor2(k,i,j),vlor3(k,i,j) enddo @@ -500,33 +583,63 @@ C enddo endif #endif +C Read of Side-chain backbone correlation parameters +C Modified 11 May 2012 by Adasko +CCC C -C 5/21/07 (AL) Read coefficients of the backbone-local sidechain-local -C correlation energies. -C - read (isccor,*,end=119,err=119) nterm_sccor - do i=1,20 - do j=1,20 - read (isccor,'(a)') - do k=1,nterm_sccor - read (isccor,*,end=119,err=119) kk,v1sccor(k,i,j), - & v2sccor(k,i,j) + read (isccor,*,end=113,err=113) nsccortyp +#ifdef SCCORPDB + read (isccor,*,end=113,err=113) (isccortyp(i),i=1,ntyp) +#else + read (isccor,*,end=113,err=113) (isccortyp(i),i=-ntyp,ntyp) +#endif +c write (iout,*) 'ntortyp',ntortyp + maxinter=3 +cc maxinter is maximum interaction sites + do l=1,maxinter + do i=1,nsccortyp + do j=1,nsccortyp + read (isccor,*,end=113,err=113) nterm_sccor(i,j),nlor_sccor(i,j) + v0ijsccor=0.0d0 + si=-1.0d0 + + do k=1,nterm_sccor(i,j) + read (isccor,*,end=113,err=113) kk,v1sccor(k,l,i,j) + & ,v2sccor(k,l,i,j) + v0ijsccor=v0ijsccor+si*v1sccor(k,l,i,j) + si=-si enddo + do k=1,nlor_sccor(i,j) + read (isccor,*,end=113,err=113) kk,vlor1sccor(k,i,j), + & vlor2sccor(k,i,j),vlor3sccor(k,i,j) + v0ijsccor=v0ijsccor+vlor1sccor(k,i,j)/ + &(1+vlor3sccor(k,i,j)**2) + enddo + v0sccor(i,j)=v0ijsccor enddo enddo + enddo close (isccor) + if (lprint) then - write (iout,'(/a/)') 'Torsional constants of SCCORR:' - do i=1,20 - do j=1,20 + write (iout,'(/a/)') 'Torsional constants:' + do i=1,nsccortyp + do j=1,nsccortyp write (iout,*) 'ityp',i,' jtyp',j - do k=1,nterm_sccor - write (iout,'(2(1pe15.5))') v1sccor(k,i,j),v2sccor(k,i,j) + write (iout,*) 'Fourier constants' + do k=1,nterm_sccor(i,j) + write (iout,'(2(1pe15.5))') v1sccor(k,l,i,j),v2sccor(k,l,i,j) + enddo + write (iout,*) 'Lorenz constants' + do k=1,nlor_sccor(i,j) + write (iout,'(3(1pe15.5))') + & vlor1sccor(k,i,j),vlor2sccor(k,i,j),vlor3sccor(k,i,j) enddo enddo enddo endif C +C C 9/18/99 (AL) Read coefficients of the Fourier expansion of the local C interaction energy of the Gly, Ala, and Pro prototypes. C @@ -535,7 +648,7 @@ C write (iout,*) "Coefficients of the cumulants" endif read (ifourier,*) nloctyp - do i=1,nloctyp + do i=0,nloctyp-1 read (ifourier,*,end=115,err=115) read (ifourier,*,end=115,err=115) (b(ii),ii=1,13) if (lprint) then @@ -544,20 +657,31 @@ C endif B1(1,i) = b(3) B1(2,i) = b(5) + B1(1,-i) = b(3) + B1(2,-i) = -b(5) c b1(1,i)=0.0d0 c b1(2,i)=0.0d0 B1tilde(1,i) = b(3) - B1tilde(2,i) =-b(5) + B1tilde(2,i) =-b(5) + B1tilde(1,-i) =-b(3) + B1tilde(2,-i) =b(5) c b1tilde(1,i)=0.0d0 c 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) + c b2(1,i)=0.0d0 c 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) c CC(1,1,i)=0.0d0 c CC(2,2,i)=0.0d0 c CC(2,1,i)=0.0d0 @@ -566,6 +690,11 @@ c CC(1,2,i)=0.0d0 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) + c Ctilde(1,1,i)=0.0d0 c Ctilde(1,2,i)=0.0d0 c Ctilde(2,1,i)=0.0d0 @@ -574,6 +703,10 @@ c Ctilde(2,2,i)=0.0d0 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) c DD(1,1,i)=0.0d0 c DD(2,2,i)=0.0d0 c DD(2,1,i)=0.0d0 @@ -582,6 +715,11 @@ c DD(1,2,i)=0.0d0 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) + c Dtilde(1,1,i)=0.0d0 c Dtilde(1,2,i)=0.0d0 c Dtilde(2,1,i)=0.0d0 @@ -590,6 +728,11 @@ c Dtilde(2,2,i)=0.0d0 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) + c ee(1,1,i)=1.0d0 c ee(2,2,i)=1.0d0 c ee(2,1,i)=0.0d0