+++ /dev/null
- subroutine chainbuild
-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'
- logical lprn
-C Set lprn=.true. for debugging
- lprn = .false.
-C
-C Define the origin and orientation of the coordinate system and locate the
-C first three CA's and SC(2).
-C
- call orig_frame
-*
-* Build the alpha-carbon chain.
-*
- do i=4,nres
- call locate_next_res(i)
- enddo
-C
-C First and last SC must coincide with the corresponding CA.
-C
- do j=1,3
- dc(j,nres+1)=0.0D0
- dc_norm(j,nres+1)=0.0D0
- dc(j,nres+nres)=0.0D0
- dc_norm(j,nres+nres)=0.0D0
- c(j,nres+1)=c(j,1)
- c(j,nres+nres)=c(j,nres)
- enddo
-*
-* Temporary diagnosis
-*
- if (lprn) then
-
- call cartprint
- write (iout,'(/a)') 'Recalculated internal coordinates'
- do i=2,nres-1
- do j=1,3
- c(j,maxres2)=0.5D0*(c(j,i-1)+c(j,i+1))
- enddo
- be=0.0D0
- if (i.gt.3) be=rad2deg*beta(i-3,i-2,i-1,i)
- be1=rad2deg*beta(nres+i,i,maxres2,i+1)
- alfai=0.0D0
- if (i.gt.2) alfai=rad2deg*alpha(i-2,i-1,i)
- write (iout,1212) restyp(itype(i)),i,dist(i-1,i),
- & alfai,be,dist(nres+i,i),rad2deg*alpha(nres+i,i,maxres2),be1
- enddo
- 1212 format (a3,'(',i3,')',2(f10.5,2f10.2))
-
- endif
-
- return
- end
-c-------------------------------------------------------------------------
- subroutine orig_frame
-C
-C Define the origin and orientation of the coordinate system and locate
-C the first three atoms.
-C
- implicit real*8 (a-h,o-z)
- include 'DIMENSIONS'
- include 'COMMON.CHAIN'
- include 'COMMON.LOCAL'
- include 'COMMON.GEO'
- include 'COMMON.VAR'
- cost=dcos(theta(3))
- sint=dsin(theta(3))
- t(1,1,1)=-cost
- t(1,2,1)=-sint
- t(1,3,1)= 0.0D0
- t(2,1,1)=-sint
- t(2,2,1)= cost
- t(2,3,1)= 0.0D0
- t(3,1,1)= 0.0D0
- t(3,2,1)= 0.0D0
- t(3,3,1)= 1.0D0
- 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
- c(1,1)=0.0D0
- c(2,1)=0.0D0
- c(3,1)=0.0D0
- c(1,2)=vbld(2)
- c(2,2)=0.0D0
- c(3,2)=0.0D0
- dc(1,0)=0.0d0
- dc(2,0)=0.0D0
- dc(3,0)=0.0D0
- dc(1,1)=vbld(2)
- dc(2,1)=0.0D0
- dc(3,1)=0.0D0
- dc_norm(1,0)=0.0D0
- dc_norm(2,0)=0.0D0
- dc_norm(3,0)=0.0D0
- dc_norm(1,1)=1.0D0
- dc_norm(2,1)=0.0D0
- 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)
- enddo
- call locate_side_chain(2)
- return
- end
-c-----------------------------------------------------------------------------
- subroutine locate_next_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)
- 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)
- c(j,i)=c(j,i-1)+dc(j,i-1)
- 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_side_chain(i)
-C
-C Locate the side-chain centroid i, 1 < i < NRES. Put in C(*,NRES+i).
-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'
- dimension xx(3)
-
-c dsci=dsc(itype(i))
-c dsci_inv=dsc_inv(itype(i))
- dsci=vbld(i+nres)
- dsci_inv=vbld_inv(i+nres)
-#ifdef OSF
- alphi=alph(i)
- omegi=omeg(i)
- if (alphi.ne.alphi) alphi=100.0
- if (omegi.ne.omegi) omegi=-100.0
-#else
- alphi=alph(i)
- omegi=omeg(i)
-#endif
- cosalphi=dcos(alphi)
- sinalphi=dsin(alphi)
- cosomegi=dcos(omegi)
- sinomegi=dsin(omegi)
- xp= dsci*cosalphi
- yp= dsci*sinalphi*cosomegi
- zp=-dsci*sinalphi*sinomegi
-* Now we have to rotate the coordinate system by 180-theta(i)/2 so as to get its
-* X-axis aligned with the vector DC(*,i)
- theta2=pi-0.5D0*theta(i+1)
- cost2=dcos(theta2)
- sint2=dsin(theta2)
- xx(1)= xp*cost2+yp*sint2
- xx(2)=-xp*sint2+yp*cost2
- xx(3)= zp
-cd print '(a3,i3,3f10.5,5x,3f10.5)',restyp(itype(i)),i,
-cd & xp,yp,zp,(xx(k),k=1,3)
- do j=1,3
- xloc(j,i)=xx(j)
- enddo
-* Bring the SC vectors to the common coordinate system.
- xx(1)=xloc(1,i)
- xx(2)=xloc(2,i)*r(2,2,i-1)+xloc(3,i)*r(2,3,i-1)
- xx(3)=xloc(2,i)*r(3,2,i-1)+xloc(3,i)*r(3,3,i-1)
- do j=1,3
- xrot(j,i)=xx(j)
- enddo
- do j=1,3
- rj=0.0D0
- do k=1,3
- rj=rj+prod(j,k,i-1)*xx(k)
- enddo
- dc(j,nres+i)=rj
- dc_norm(j,nres+i)=rj*dsci_inv
- c(j,nres+i)=c(j,i)+rj
- enddo
- return
- end
projects / unres.git / blobdiff