From d209eee3dec438628ee9d5a9c990ad9ca9dec1c5 Mon Sep 17 00:00:00 2001 From: Adam Kazimierz Sieradzan Date: Mon, 9 Jul 2012 03:46:21 -0400 Subject: [PATCH] D i L aminokwasy tuz przed testami --- source/unres/src_MD/COMMON.TORSION | 14 ++-- source/unres/src_MD/cinfo.f | 6 +- source/unres/src_MD/energy_p_new_barrier.F | 22 +++--- source/unres/src_MD/initialize_p.F | 24 ++++++- source/unres/src_MD/parmread.F | 102 +++++++++++++++++----------- source/wham/src/energy_p_new.F | 15 +++- source/wham/src/parmread.F | 9 +-- 7 files changed, 129 insertions(+), 63 deletions(-) diff --git a/source/unres/src_MD/COMMON.TORSION b/source/unres/src_MD/COMMON.TORSION index 2ceb636..3c9ae39 100644 --- a/source/unres/src_MD/COMMON.TORSION +++ b/source/unres/src_MD/COMMON.TORSION @@ -13,11 +13,15 @@ C Torsional constants of the rotation about virtual-bond dihedral angles C 6/23/01 - constants for double torsionals double precision v1c,v1s,v2c,v2s integer ntermd_1,ntermd_2 - common /torsiond/ v1c(2,maxtermd_1,maxtor,maxtor,maxtor), - & v1s(2,maxtermd_1,maxtor,maxtor,maxtor), - & v2c(maxtermd_2,maxtermd_2,maxtor,maxtor,maxtor), - & v2s(maxtermd_2,maxtermd_2,maxtor,maxtor,maxtor), - & ntermd_1(maxtor,maxtor,maxtor),ntermd_2(maxtor,maxtor,maxtor) + common /torsiond/ + &v1c(2,maxtermd_1,-maxtor:maxtor,-maxtor:maxtor,-maxtor:maxtor,2), + &v1s(2,maxtermd_1,-maxtor:maxtor,-maxtor:maxtor,-maxtor:maxtor,2), + &v2c(maxtermd_2,maxtermd_2,-maxtor:maxtor,-maxtor:maxtor, + & -maxtor:maxtor,2), + &v2s(maxtermd_2,maxtermd_2,-maxtor:maxtor,-maxtor:maxtor, + & -maxtor:maxtor,2), + & ntermd_1(-maxtor:maxtor,-maxtor:maxtor,-maxtor:maxtor,2), + & ntermd_2(-maxtor:maxtor,-maxtor:maxtor,-maxtor:maxtor,2) C 9/18/99 - added Fourier coeffficients of the expansion of local energy C surface double precision b1,b2,cc,dd,ee,ctilde,dtilde,b2tilde diff --git a/source/unres/src_MD/cinfo.f b/source/unres/src_MD/cinfo.f index c5dc2ce..89171a1 100644 --- a/source/unres/src_MD/cinfo.f +++ b/source/unres/src_MD/cinfo.f @@ -1,10 +1,10 @@ C DO NOT EDIT THIS FILE - IT HAS BEEN GENERATED BY COMPINFO.C -C 2 5 336 +C 2 5 341 subroutine cinfo include 'COMMON.IOUNITS' write(iout,*)'++++ Compile info ++++' - write(iout,*)'Version 2.5 build 336' - write(iout,*)'compiled Thu Jul 5 08:53:57 2012' + write(iout,*)'Version 2.5 build 341' + write(iout,*)'compiled Mon Jul 9 03:40:18 2012' write(iout,*)'compiled by aks255@matrix.chem.cornell.edu' write(iout,*)'OS name: Linux ' write(iout,*)'OS release: 2.6.34.9-69.fc13.x86_64 ' diff --git a/source/unres/src_MD/energy_p_new_barrier.F b/source/unres/src_MD/energy_p_new_barrier.F index 87555f9..31584d0 100644 --- a/source/unres/src_MD/energy_p_new_barrier.F +++ b/source/unres/src_MD/energy_p_new_barrier.F @@ -5873,15 +5873,17 @@ c lprn=.true. itori=itortyp(itype(i-2)) itori1=itortyp(itype(i-1)) itori2=itortyp(itype(i)) + iblock=1 + if (iabs(itype(i+1).eq.20)) iblock=2 phii=phi(i) phii1=phi(i+1) gloci1=0.0D0 gloci2=0.0D0 - do j=1,ntermd_1(itori,itori1,itori2) - v1cij=v1c(1,j,itori,itori1,itori2) - v1sij=v1s(1,j,itori,itori1,itori2) - v2cij=v1c(2,j,itori,itori1,itori2) - v2sij=v1s(2,j,itori,itori1,itori2) + do j=1,ntermd_1(itori,itori1,itori2,iblock) + v1cij=v1c(1,j,itori,itori1,itori2,iblock) + v1sij=v1s(1,j,itori,itori1,itori2,iblock) + v2cij=v1c(2,j,itori,itori1,itori2,iblock) + v2sij=v1s(2,j,itori,itori1,itori2,iblock) cosphi1=dcos(j*phii) sinphi1=dsin(j*phii) cosphi2=dcos(j*phii1) @@ -5891,12 +5893,12 @@ c lprn=.true. gloci1=gloci1+j*(v1sij*cosphi1-v1cij*sinphi1) gloci2=gloci2+j*(v2sij*cosphi2-v2cij*sinphi2) enddo - do k=2,ntermd_2(itori,itori1,itori2) + do k=2,ntermd_2(itori,itori1,itori2,iblock) do l=1,k-1 - v1cdij = v2c(k,l,itori,itori1,itori2) - v2cdij = v2c(l,k,itori,itori1,itori2) - v1sdij = v2s(k,l,itori,itori1,itori2) - v2sdij = v2s(l,k,itori,itori1,itori2) + v1cdij = v2c(k,l,itori,itori1,itori2,iblock) + v2cdij = v2c(l,k,itori,itori1,itori2,iblock) + v1sdij = v2s(k,l,itori,itori1,itori2,iblock) + v2sdij = v2s(l,k,itori,itori1,itori2,iblock) cosphi1p2=dcos(l*phii+(k-l)*phii1) cosphi1m2=dcos(l*phii-(k-l)*phii1) sinphi1p2=dsin(l*phii+(k-l)*phii1) diff --git a/source/unres/src_MD/initialize_p.F b/source/unres/src_MD/initialize_p.F index 8880628..62706fb 100644 --- a/source/unres/src_MD/initialize_p.F +++ b/source/unres/src_MD/initialize_p.F @@ -191,10 +191,10 @@ c call memmon_print_usage() enddo nlob(ntyp1)=0 dsc(ntyp1)=0.0D0 - do i=1,maxtor + do i=-maxtor,maxtor itortyp(i)=0 do iblock=1,2 - do j=1,maxtor + do j=-maxtor,maxtor do k=1,maxterm v1(k,j,i,iblock)=0.0D0 v2(k,j,i,iblock)=0.0D0 @@ -202,6 +202,26 @@ c call memmon_print_usage() enddo enddo enddo + do iblock=1,2 + do i=-maxtor,maxtor + do j=-maxtor,maxtor + do k=-maxtor,maxtor + do l=1,maxtermd_1 + v1c(1,l,i,j,k,iblock)=0.0D0 + v1s(1,l,i,j,k,iblock)=0.0D0 + v1c(2,l,i,j,k,iblock)=0.0D0 + v1s(2,l,i,j,k,iblock)=0.0D0 + enddo !l + do l=1,maxtermd_2 + do m=1,maxtermd_2 + v2c(m,l,i,j,k,iblock)=0.0D0 + v2s(m,l,i,j,k,iblock)=0.0D0 + enddo !m + enddo !l + enddo !k + enddo !j + enddo !i + enddo !iblock do i=1,maxres itype(i)=0 itel(i)=0 diff --git a/source/unres/src_MD/parmread.F b/source/unres/src_MD/parmread.F index 2e953a2..942a463 100644 --- a/source/unres/src_MD/parmread.F +++ b/source/unres/src_MD/parmread.F @@ -28,6 +28,7 @@ C include 'COMMON.SETUP' character*1 t1,t2,t3 character*1 onelett(4) /"G","A","P","D"/ + character*1 toronelet(-2:2) /"p","a","G","A","P"/ logical lprint,LaTeX dimension blower(3,3,maxlob) dimension b(13) @@ -470,7 +471,7 @@ C do i=-ntyp,-1 itortyp(i)=-itortyp(-i) enddo - write (iout,*) 'ntortyp',ntortyp +c 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), @@ -486,7 +487,7 @@ C 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) +c write(iout,*) i,j,k,iblock,nterm(i,j,iblock),v1(k,-i,-j,iblock) enddo do k=1,nlor(i,j,iblock) read (itorp,*,end=113,err=113) kk,vlor1(k,i,j), @@ -520,12 +521,16 @@ C C C 6/23/01 Read parameters for double torsionals C - do i=1,ntortyp - do j=1,ntortyp - do k=1,ntortyp + do iblock=1,2 + do i=0,ntortyp-1 + do j=-ntortyp+1,ntortyp-1 + do k=-ntortyp+1,ntortyp-1 read (itordp,'(3a1)',end=114,err=114) t1,t2,t3 - if (t1.ne.onelett(i) .or. t2.ne.onelett(j) - & .or. t3.ne.onelett(k)) then + write (iout,*) "OK onelett", + & i,j,k,t1,t2,t3 + + if (t1.ne.toronelet(i) .or. t2.ne.toronelet(j) + & .or. t3.ne.toronelet(k)) then write (iout,*) "Error in double torsional parameter file", & i,j,k,t1,t2,t3 #ifdef MPI @@ -533,55 +538,76 @@ C #endif stop "Error in double torsional parameter file" endif - read (itordp,*,end=114,err=114) ntermd_1(i,j,k), - & ntermd_2(i,j,k) - read (itordp,*,end=114,err=114) (v1c(1,l,i,j,k),l=1, - & ntermd_1(i,j,k)) - read (itordp,*,end=114,err=114) (v1s(1,l,i,j,k),l=1, - & ntermd_1(i,j,k)) - read (itordp,*,end=114,err=114) (v1c(2,l,i,j,k),l=1, - & ntermd_1(i,j,k)) - read (itordp,*,end=114,err=114) (v1s(2,l,i,j,k),l=1, - & ntermd_1(i,j,k)) - read (itordp,*,end=114,err=114) ((v2c(l,m,i,j,k), - & v2c(m,l,i,j,k),v2s(l,m,i,j,k),v2s(m,l,i,j,k), - & m=1,l-1),l=1,ntermd_2(i,j,k)) - enddo - enddo - enddo - if (lprint) then + read (itordp,*,end=114,err=114) ntermd_1(i,j,k,iblock), + & ntermd_2(i,j,k,iblock) + read (itordp,*,end=114,err=114) (v1c(1,l,i,j,k,iblock),l=1, + & ntermd_1(i,j,k,iblock)) + read (itordp,*,end=114,err=114) (v1s(1,l,i,j,k,iblock),l=1, + & ntermd_1(i,j,k,iblock)) + read (itordp,*,end=114,err=114) (v1c(2,l,i,j,k,iblock),l=1, + & ntermd_1(i,j,k,iblock)) + read (itordp,*,end=114,err=114) (v1s(2,l,i,j,k,iblock),l=1, + & ntermd_1(i,j,k,iblock)) +C Martix of D parameters for one dimesional foureir series + do l=1, ntermd_1(i,j,k,iblock) + v1c(1,l,-i,-j,-k,iblock)=v1c(1,l,i,j,k,iblock) + v1s(1,l,-i,-j,-k,iblock)=-v1s(1,l,i,j,k,iblock) + v1c(2,l,-i,-j,-k,iblock)=v1c(2,l,i,j,k,iblock) + v1s(2,l,-i,-j,-k,iblock)=-v1s(2,l,i,j,k,iblock) + enddo + read (itordp,*,end=114,err=114) ((v2c(l,m,i,j,k,iblock), + & v2c(m,l,i,j,k,iblock),v2s(l,m,i,j,k,iblock), + & v2s(m,l,i,j,k,iblock), + & m=1,l-1),l=1,ntermd_2(i,j,k,iblock)) +C Martix of D parameters for two dimesional fourier series + do l=1,ntermd_2(i,j,k,iblock) + do m=1,l-1 + v2c(l,m,-i,-j,-k,iblock)=v2c(l,m,i,j,k,iblock) + v2c(m,l,-i,-j,-k,iblock)=v2c(m,l,i,j,k,iblock) + v2s(l,m,-i,-j,-k,iblock)=-v2s(l,m,i,j,k,iblock) + v2s(m,l,-i,-j,-k,iblock)=-v2s(m,l,i,j,k,iblock) + enddo!m + enddo!l + enddo!k + enddo!j + enddo!i + enddo!iblock +cc if (lprint) then write (iout,*) write (iout,*) 'Constants for double torsionals' do i=1,ntortyp - do j=1,ntortyp - do k=1,ntortyp + do j=-ntortyp,ntortyp + do k=-ntortyp,ntortyp write (iout,*) 'ityp',i,' jtyp',j,' ktyp',k, - & ' nsingle',ntermd_1(i,j,k),' ndouble',ntermd_2(i,j,k) + & ' nsingle',ntermd_1(i,j,k,iblock), + & ' ndouble',ntermd_2(i,j,k,iblock) write (iout,*) write (iout,*) 'Single angles:' - do l=1,ntermd_1(i,j,k) - write (iout,'(i5,2f10.5,5x,2f10.5)') l, - & v1c(1,l,i,j,k),v1s(1,l,i,j,k), - & v1c(2,l,i,j,k),v1s(2,l,i,j,k) + do l=1,ntermd_1(i,j,k,iblock) + write (iout,'(i5,2f10.5,5x,2f10.5,5x,2f10.5)') l, + & v1c(1,l,i,j,k,iblock),v1s(1,l,i,j,k,iblock), + & v1c(2,l,i,j,k,iblock),v1s(2,l,i,j,k,iblock), + & v1s(1,l,-i,-j,-k,iblock),v1s(2,l,-i,-j,-k,iblock) enddo write (iout,*) write (iout,*) 'Pairs of angles:' - write (iout,'(3x,20i10)') (l,l=1,ntermd_2(i,j,k)) - do l=1,ntermd_2(i,j,k) + write (iout,'(3x,20i10)') (l,l=1,ntermd_2(i,j,k,iblock)) + do l=1,ntermd_2(i,j,k,iblock) write (iout,'(i5,20f10.5)') - & l,(v2c(l,m,i,j,k),m=1,ntermd_2(i,j,k)) + & l,(v2c(l,m,i,j,k,iblock),m=1,ntermd_2(i,j,k,iblock)) enddo write (iout,*) - write (iout,'(3x,20i10)') (l,l=1,ntermd_2(i,j,k)) - do l=1,ntermd_2(i,j,k) + write (iout,'(3x,20i10)') (l,l=1,ntermd_2(i,j,k,iblock)) + do l=1,ntermd_2(i,j,k,iblock) write (iout,'(i5,20f10.5)') - & l,(v2s(l,m,i,j,k),m=1,ntermd_2(i,j,k)) + & l,(v2s(l,m,i,j,k,iblock),m=1,ntermd_2(i,j,k,iblock)), + & (v2s(l,m,-i,-j,-k,iblock),m=1,ntermd_2(i,j,k,iblock)) enddo write (iout,*) enddo enddo enddo - endif +cc endif #endif C Read of Side-chain backbone correlation parameters C Modified 11 May 2012 by Adasko diff --git a/source/wham/src/energy_p_new.F b/source/wham/src/energy_p_new.F index 27f9010..4b2dc0c 100644 --- a/source/wham/src/energy_p_new.F +++ b/source/wham/src/energy_p_new.F @@ -4463,16 +4463,24 @@ c lprn=.true. itori=itortyp(itype(i-2)) itori1=itortyp(itype(i-1)) itori2=itortyp(itype(i)) +c iblock=1 +c if (iabs(itype(i+1)).eq.20) iblock=2 phii=phi(i) phii1=phi(i+1) gloci1=0.0D0 gloci2=0.0D0 C Regular cosine and sine terms - do j=1,ntermd_1(itori,itori1,itori2) +c c do j=1,ntermd_1(itori,itori1,itori2,iblock) +c v1cij=v1c(1,j,itori,itori1,itori2,iblock) +c v1sij=v1s(1,j,itori,itori1,itori2,iblock) +c v2cij=v1c(2,j,itori,itori1,itori2,iblock) +c v2sij=v1s(2,j,itori,itori1,itori2,iblock) + do j=1,ntermd_1(itori,itori1,itori2) v1cij=v1c(1,j,itori,itori1,itori2) v1sij=v1s(1,j,itori,itori1,itori2) v2cij=v1c(2,j,itori,itori1,itori2) v2sij=v1s(2,j,itori,itori1,itori2) + cosphi1=dcos(j*phii) sinphi1=dsin(j*phii) cosphi2=dcos(j*phii1) @@ -4483,7 +4491,12 @@ C Regular cosine and sine terms gloci2=gloci2+j*(v2sij*cosphi2-v2cij*sinphi2) enddo do k=2,ntermd_2(itori,itori1,itori2) +c do k=2,ntermd_2(itori,itori1,itori2,iblock) do l=1,k-1 +c v1cdij = v2c(k,l,itori,itori1,itori2,iblock) +c v2cdij = v2c(l,k,itori,itori1,itori2,iblock) +c v1sdij = v2s(k,l,itori,itori1,itori2,iblock) +c v2sdij = v2s(l,k,itori,itori1,itori2,iblock) v1cdij = v2c(k,l,itori,itori1,itori2) v2cdij = v2c(l,k,itori,itori1,itori2) v1sdij = v2s(k,l,itori,itori1,itori2) diff --git a/source/wham/src/parmread.F b/source/wham/src/parmread.F index 9b5e224..d8d7817 100644 --- a/source/wham/src/parmread.F +++ b/source/wham/src/parmread.F @@ -23,6 +23,7 @@ C include 'COMMON.FREE' character*1 t1,t2,t3 character*1 onelett(4) /"G","A","P","D"/ + character*1 toronelet(-2:2)/"p","a","G","A","P"/ logical lprint dimension blower(3,3,maxlob) character*800 controlcard @@ -528,12 +529,12 @@ C C C 6/23/01 Read parameters for double torsionals C - do i=1,ntortyp - do j=1,ntortyp + do i=0,ntortyp-1 + do j=-ntortyp,ntortyp do k=1,ntortyp read (itordp,'(3a1)') t1,t2,t3 - if (t1.ne.onelett(i) .or. t2.ne.onelett(j) - & .or. t3.ne.onelett(k)) then + if (t1.ne.toronelet(i) .or. t2.ne.toronelet(j) + & .or. t3.ne.toronelet(k)) then write (iout,*) "Error in double torsional parameter file", & i,j,k,t1,t2,t3 stop "Error in double torsional parameter file" -- 1.7.9.5