X-Git-Url: http://mmka.chem.univ.gda.pl/gitweb/?a=blobdiff_plain;f=source%2Funres%2Fsrc_MD-M%2Fchainbuild.F;h=1261b4a605d3d9e6b9357b798000ba2783f17220;hb=34d3ad3987785642be58fb2f26557d3314215577;hp=45a1a53837e28da1c8198f61d4d9973d13076818;hpb=f690e8b70bab14132839afebf080d4a28363b226;p=unres.git diff --git a/source/unres/src_MD-M/chainbuild.F b/source/unres/src_MD-M/chainbuild.F index 45a1a53..1261b4a 100644 --- a/source/unres/src_MD-M/chainbuild.F +++ b/source/unres/src_MD-M/chainbuild.F @@ -12,13 +12,37 @@ C include 'COMMON.IOUNITS' include 'COMMON.NAMES' include 'COMMON.INTERACT' - logical lprn + double precision e1(3),e2(3),e3(3) + logical lprn,perbox,fail C Set lprn=.true. for debugging lprn = .false. + perbox=.false. + fail=.false. + call chainbuild_cart + return + end +C#ifdef DEBUG +C if (perbox) then +C first three CAs and SC(2). C -C Define the origin and orientation of the coordinate system and locate the -C first three CA's and SC(2). + subroutine chainbuild_extconf +C +C Build the virtual polypeptide chain. Side-chain centroids are moveable. +C As of 2/17/95. C + implicit real*8 (a-h,o-z) + include 'DIMENSIONS' + include 'COMMON.CHAIN' + include 'COMMON.LOCAL' + include 'COMMON.GEO' + include 'COMMON.VAR' + include 'COMMON.IOUNITS' + include 'COMMON.NAMES' + include 'COMMON.INTERACT' + double precision e1(3),e2(3),e3(3) + logical lprn /.false./,perbox,fail + +c write (iout,*) "Calling chainbuild_extconf" call orig_frame * * Build the alpha-carbon chain. @@ -43,6 +67,12 @@ C if (lprn) then call cartprint + write (iout,*) 'dc_norm' + do i=1,nres + write (iout,'(a3,1x,i3,3f10.5,5x,3f10.5)') + & restyp(itype(i)),i,(dc_norm(j,i),j=1,3), + & (dc_norm(j,i+nres),j=1,3) + enddo write (iout,'(/a)') 'Recalculated internal coordinates' do i=2,nres-1 do j=1,3 @@ -58,10 +88,11 @@ C enddo 1212 format (a3,'(',i3,')',2(f10.5,2f10.2)) +C endif endif - return end +C#endif c------------------------------------------------------------------------- subroutine orig_frame C @@ -126,13 +157,86 @@ C dc_norm(3,1)=0.0D0 do j=1,3 dc_norm(j,2)=prod(j,1,2) - dc(j,2)=vbld(3)*prod(j,1,2) - c(j,3)=c(j,2)+dc(j,2) + dc(j,2)=vbld(3)*prod(j,1,2) + c(j,3)=c(j,2)+dc(j,2) enddo call locate_side_chain(2) return end c----------------------------------------------------------------------------- + subroutine locate_prev_res(i) +C +C Locate CA(i) and SC(i-1) +C + implicit real*8 (a-h,o-z) + include 'DIMENSIONS' + include 'COMMON.CHAIN' + include 'COMMON.LOCAL' + include 'COMMON.GEO' + include 'COMMON.VAR' + include 'COMMON.IOUNITS' + include 'COMMON.NAMES' + include 'COMMON.INTERACT' +C +C Define the rotation matrices corresponding to CA(i) +C +#ifdef OSF + theti=theta(i+2) + if (theti.ne.theti) theti=100.0 + phii=phi(i+3) + if (phii.ne.phii) phii=180.0 +#else + theti=theta(i+2) + phii=phi(i+3) +#endif + cost=dcos(theti) + sint=dsin(theti) + cosphi=dcos(phii) + sinphi=dsin(phii) +* Define the matrices of the rotation about the virtual-bond valence angles +* theta, T(i,j,k), virtual-bond dihedral angles gamma (miscalled PHI in this +* program), R(i,j,k), and, the cumulative matrices of rotation RT + t(1,1,i+2)=-cost + t(1,2,i+2)=-sint + t(1,3,i+2)= 0.0D0 + t(2,1,i+2)=-sint + t(2,2,i+2)= cost + t(2,3,i+2)= 0.0D0 + t(3,1,i+2)= 0.0D0 + t(3,2,i+2)= 0.0D0 + t(3,3,i+2)= 1.0D0 + r(1,1,i+2)= 1.0D0 + r(1,2,i+2)= 0.0D0 + r(1,3,i+2)= 0.0D0 + r(2,1,i+2)= 0.0D0 + r(2,2,i+2)=-cosphi + r(2,3,i+2)= sinphi + r(3,1,i+2)= 0.0D0 + r(3,2,i+2)= sinphi + r(3,3,i+2)= cosphi + rt(1,1,i+2)=-cost + rt(1,2,i+2)=-sint + rt(1,3,i+2)=0.0D0 + rt(2,1,i+2)=sint*cosphi + rt(2,2,i+2)=-cost*cosphi + rt(2,3,i+2)=sinphi + rt(3,1,i+2)=-sint*sinphi + rt(3,2,i+2)=cost*sinphi + rt(3,3,i+2)=cosphi + call matmult(prod(1,1,i+2),rt(1,1,i+2),prod(1,1,i+1)) + do j=1,3 + dc_norm(j,i)=-prod(j,1,i+1) + dc(j,i)=-vbld(i)*prod(j,1,i+1) + c(j,i)=c(j,i+1)+dc(j,i) + enddo +cd print '(2i3,2(3f10.5,5x))', i-1,i,(dc(j,i+1),j=1,3),(c(j,i),j=1,3) +C +C Now calculate the coordinates of SC(i+1) +C + call locate_side_chain(i+1) + return + end +c----------------------------------------------------------------------------- subroutine locate_next_res(i) C C Locate CA(i) and SC(i-1) @@ -272,3 +376,255 @@ cd & xp,yp,zp,(xx(k),k=1,3) enddo return end +c------------------------------------------ + subroutine returnbox + include 'DIMENSIONS' +#ifdef MPI + include 'mpif.h' +#endif + include 'COMMON.CONTROL' + include 'COMMON.VAR' + include 'COMMON.MD' +#ifndef LANG0 + include 'COMMON.LANGEVIN' +#else + include 'COMMON.LANGEVIN.lang0' +#endif + include 'COMMON.CHAIN' + include 'COMMON.DERIV' + include 'COMMON.GEO' + include 'COMMON.LOCAL' + include 'COMMON.INTERACT' + include 'COMMON.IOUNITS' + include 'COMMON.NAMES' + include 'COMMON.TIME1' + include 'COMMON.REMD' + include 'COMMON.SETUP' + include 'COMMON.MUCA' + include 'COMMON.HAIRPIN' +C change suggested by Ana - begin + integer allareout +C change suggested by Ana - end + j=1 + chain_beg=1 +C do i=1,nres +C write(*,*) 'initial', i,j,c(j,i) +C enddo +C change suggested by Ana - begin + allareout=1 +C change suggested by Ana -end + do i=1,nres-1 + if ((itype(i).eq.ntyp1).and.(itype(i+1).eq.ntyp1)) then + chain_end=i + if (allareout.eq.1) then + ireturnval=int(c(j,i)/boxxsize) + if (c(j,i).le.0) ireturnval=ireturnval-1 + do k=chain_beg,chain_end + c(j,k)=c(j,k)-ireturnval*boxxsize + c(j,k+nres)=c(j,k+nres)-ireturnval*boxxsize + enddo +C Suggested by Ana + if (chain_beg.eq.1) + & dc_old(1,0)=dc_old(1,0)-ireturnval*boxxsize +C Suggested by Ana -end + endif + chain_beg=i+1 + allareout=1 + else + if (int(c(j,i)/boxxsize).eq.0) allareout=0 + endif + enddo + if (allareout.eq.1) then + ireturnval=int(c(j,i)/boxxsize) + if (c(j,i).le.0) ireturnval=ireturnval-1 + do k=chain_beg,nres + c(j,k)=c(j,k)-ireturnval*boxxsize + c(j,k+nres)=c(j,k+nres)-ireturnval*boxxsize + enddo + endif +C NO JUMP +C do i=1,nres +C write(*,*) 'befor no jump', i,j,c(j,i) +C enddo + nojumpval=0 + do i=2,nres + if (itype(i).eq.ntyp1 .and. itype(i-1).eq.ntyp1) then + difference=abs(c(j,i-1)-c(j,i)) +C print *,'diff', difference + if (difference.gt.boxxsize/2.0) then + if (c(j,i-1).gt.c(j,i)) then + nojumpval=1 + else + nojumpval=-1 + endif + else + nojumpval=0 + endif + endif + c(j,i)=c(j,i)+nojumpval*boxxsize + c(j,i+nres)=c(j,i+nres)+nojumpval*boxxsize + enddo + nojumpval=0 + do i=2,nres + if (itype(i).eq.ntyp1 .and. itype(i-1).eq.ntyp1) then + difference=abs(c(j,i-1)-c(j,i)) + if (difference.gt.boxxsize/2.0) then + if (c(j,i-1).gt.c(j,i)) then + nojumpval=1 + else + nojumpval=-1 + endif + else + nojumpval=0 + endif + endif + c(j,i)=c(j,i)+nojumpval*boxxsize + c(j,i+nres)=c(j,i+nres)+nojumpval*boxxsize + enddo + +C do i=1,nres +C write(*,*) 'after no jump', i,j,c(j,i) +C enddo + +C NOW Y dimension +C suggesed by Ana begins + allareout=1 +C suggested by Ana ends + j=2 + chain_beg=1 + do i=1,nres-1 + if ((itype(i).eq.ntyp1).and.(itype(i+1).eq.ntyp1)) then + chain_end=i + if (allareout.eq.1) then + ireturnval=int(c(j,i)/boxysize) + if (c(j,i).le.0) ireturnval=ireturnval-1 + do k=chain_beg,chain_end + c(j,k)=c(j,k)-ireturnval*boxysize + c(j,k+nres)=c(j,k+nres)-ireturnval*boxysize + enddo +C Suggested by Ana + if (chain_beg.eq.1) + & dc_old(1,0)=dc_old(1,0)-ireturnval*boxxsize +C Suggested by Ana -end + endif + chain_beg=i+1 + allareout=1 + else + if (int(c(j,i)/boxysize).eq.0) allareout=0 + endif + enddo + if (allareout.eq.1) then + ireturnval=int(c(j,i)/boxysize) + if (c(j,i).le.0) ireturnval=ireturnval-1 + do k=chain_beg,nres + c(j,k)=c(j,k)-ireturnval*boxysize + c(j,k+nres)=c(j,k+nres)-ireturnval*boxysize + enddo + endif + nojumpval=0 + do i=2,nres + if (itype(i).eq.ntyp1 .and. itype(i-1).eq.ntyp1) then + difference=abs(c(j,i-1)-c(j,i)) + if (difference.gt.boxysize/2.0) then + if (c(j,i-1).gt.c(j,i)) then + nojumpval=1 + else + nojumpval=-1 + endif + else + nojumpval=0 + endif + endif + c(j,i)=c(j,i)+nojumpval*boxysize + c(j,i+nres)=c(j,i+nres)+nojumpval*boxysize + enddo + nojumpval=0 + do i=2,nres + if (itype(i).eq.ntyp1 .and. itype(i-1).eq.ntyp1) then + difference=abs(c(j,i-1)-c(j,i)) + if (difference.gt.boxysize/2.0) then + if (c(j,i-1).gt.c(j,i)) then + nojumpval=1 + else + nojumpval=-1 + endif + else + nojumpval=0 + endif + endif + c(j,i)=c(j,i)+nojumpval*boxysize + c(j,i+nres)=c(j,i+nres)+nojumpval*boxysize + enddo +C Now Z dimension +C Suggested by Ana -begins + allareout=1 +C Suggested by Ana -ends + j=3 + chain_beg=1 + do i=1,nres-1 + if ((itype(i).eq.ntyp1).and.(itype(i+1).eq.ntyp1)) then + chain_end=i + if (allareout.eq.1) then + ireturnval=int(c(j,i)/boxysize) + if (c(j,i).le.0) ireturnval=ireturnval-1 + do k=chain_beg,chain_end + c(j,k)=c(j,k)-ireturnval*boxzsize + c(j,k+nres)=c(j,k+nres)-ireturnval*boxzsize + enddo +C Suggested by Ana + if (chain_beg.eq.1) + & dc_old(1,0)=dc_old(1,0)-ireturnval*boxxsize +C Suggested by Ana -end + endif + chain_beg=i+1 + allareout=1 + else + if (int(c(j,i)/boxzsize).eq.0) allareout=0 + endif + enddo + if (allareout.eq.1) then + ireturnval=int(c(j,i)/boxzsize) + if (c(j,i).le.0) ireturnval=ireturnval-1 + do k=chain_beg,nres + c(j,k)=c(j,k)-ireturnval*boxzsize + c(j,k+nres)=c(j,k+nres)-ireturnval*boxzsize + enddo + endif + nojumpval=0 + do i=2,nres + if (itype(i).eq.ntyp1 .and. itype(i-1).eq.ntyp1) then + difference=abs(c(j,i-1)-c(j,i)) + if (difference.gt.(boxzsize/2.0)) then + if (c(j,i-1).gt.c(j,i)) then + nojumpval=1 + else + nojumpval=-1 + endif + else + nojumpval=0 + endif + endif + c(j,i)=c(j,i)+nojumpval*boxzsize + c(j,i+nres)=c(j,i+nres)+nojumpval*boxzsize + enddo + nojumpval=0 + do i=2,nres + if (itype(i).eq.ntyp1 .and. itype(i-1).eq.ntyp1) then + difference=abs(c(j,i-1)-c(j,i)) + if (difference.gt.boxzsize/2.0) then + if (c(j,i-1).gt.c(j,i)) then + nojumpval=1 + else + nojumpval=-1 + endif + else + nojumpval=0 + endif + endif + c(j,i)=c(j,i)+nojumpval*boxzsize + c(j,i+nres)=c(j,i+nres)+nojumpval*boxzsize + enddo + + return + end +