X-Git-Url: http://mmka.chem.univ.gda.pl/gitweb/?a=blobdiff_plain;f=source%2Funres%2Fsrc_MD-M%2Fchainbuild.F;h=a0fe42c58ad3432a1502a0c8c56565d2ad8114aa;hb=7d64cc3ff0edffb6aa37e309e4375f58bd5875a2;hp=766e14a6861e27db3fdb50d1f7be7c04d6a3183e;hpb=d8f9706208157e3247e3800d62272fe69ea06a7f;p=unres.git diff --git a/source/unres/src_MD-M/chainbuild.F b/source/unres/src_MD-M/chainbuild.F index 766e14a..a0fe42c 100644 --- a/source/unres/src_MD-M/chainbuild.F +++ b/source/unres/src_MD-M/chainbuild.F @@ -19,119 +19,30 @@ C Set lprn=.true. for debugging perbox=.false. fail=.false. print *, 'enter chainbuild' - if (perbox) then - cost=dcos(theta(3)) - sint=dsin(theta(3)) - print *,'before refsys' - call refsys(2,3,4,e1,e2,e3,fail) - print *,'after refsys' - if (fail) then - e2(1)=0.0d0 - e2(2)=1.0d0 - e2(3)=0.0d0 - endif - dc(1,0)=c(1,1) - dc(2,0)=c(2,1) - dc(3,0)=c(3,1) - print *,'dc',dc(1,0),dc(2,0),dc(3,0) - dc(1,1)=c(1,2)-c(1,1) - dc(2,1)=c(2,2)-c(2,1) - dc(3,1)=c(3,2)-c(3,1) - dc(1,2)=c(1,3)-c(1,2) - dc(2,2)=c(2,3)-c(2,2) - dc(3,2)=c(3,3)-c(3,2) - t(1,1,1)=e1(1) - t(1,2,1)=e1(2) - t(1,3,1)=e1(3) - t(2,1,1)=e2(1) - t(2,2,1)=e2(2) - t(2,3,1)=e2(3) - t(3,1,1)=e3(1) - t(3,2,1)=e3(2) - t(3,3,1)=e3(3) - veclen=0.0d0 - do i=1,3 - veclen=veclen+(c(i,2)-c(i,1))**2 - enddo - veclen=sqrt(veclen) - r(1,1,1)= 1.0D0 - r(1,2,1)= 0.0D0 - r(1,3,1)= 0.0D0 - r(2,1,1)= 0.0D0 - r(2,2,1)= 1.0D0 - r(2,3,1)= 0.0D0 - r(3,1,1)= 0.0D0 - r(3,2,1)= 0.0D0 - r(3,3,1)= 1.0D0 - do i=1,3 - do j=1,3 - rt(i,j,1)=t(i,j,1) - enddo - enddo - do i=1,3 - do j=1,3 - prod(i,j,1)=0.0D0 - prod(i,j,2)=t(i,j,1) - enddo - prod(i,i,1)=1.0D0 - enddo - call locate_side_chain(2) - do i=4,nres -#ifdef OSF - theti=theta(i) - if (theti.ne.theti) theti=100.0 - phii=phi(i) - if (phii.ne.phii) phii=180.0 -#else - theti=theta(i) - phii=phi(i) -#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-1)=prod(j,1,i-1) - dc(j,i-1)=vbld(i)*prod(j,1,i-1) - enddo - call locate_side_chain(i-1) - enddo - else -C -C Define the origin and orientation of the coordinate system and locate the + call chainbuild_cart + return + end +C#ifdef DEBUG +C if (perbox) then C first three CA's and SC(2). C + 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,perbox,fail + call orig_frame * * Build the alpha-carbon chain. @@ -171,10 +82,11 @@ C enddo 1212 format (a3,'(',i3,')',2(f10.5,2f10.2)) - endif +C endif endif return end +C#endif c------------------------------------------------------------------------- subroutine orig_frame C @@ -385,3 +297,255 @@ 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 +