--- /dev/null
+ subroutine readpdb
+C Read the PDB file and convert the peptide geometry into virtual-chain
+C geometry.
+ implicit real*8 (a-h,o-z)
+ include 'DIMENSIONS'
+ include 'COMMON.LOCAL'
+ include 'COMMON.VAR'
+ include 'COMMON.CHAIN'
+ include 'COMMON.INTERACT'
+ include 'COMMON.IOUNITS'
+ include 'COMMON.GEO'
+ include 'COMMON.NAMES'
+ include 'COMMON.CONTROL'
+ include 'COMMON.DISTFIT'
+ include 'COMMON.SETUP'
+ character*3 seq,atom,res
+ character*80 card
+ dimension sccor(3,20)
+ double precision e1(3),e2(3),e3(3)
+ logical fail
+ integer rescode
+ ibeg=1
+ lsecondary=.false.
+ nhfrag=0
+ nbfrag=0
+ do i=1,10000
+ read (ipdbin,'(a80)',end=10) card
+ if (card(:5).eq.'HELIX') then
+ nhfrag=nhfrag+1
+ lsecondary=.true.
+ read(card(22:25),*) hfrag(1,nhfrag)
+ read(card(34:37),*) hfrag(2,nhfrag)
+ endif
+ if (card(:5).eq.'SHEET') then
+ nbfrag=nbfrag+1
+ lsecondary=.true.
+ read(card(24:26),*) bfrag(1,nbfrag)
+ read(card(35:37),*) bfrag(2,nbfrag)
+crc----------------------------------------
+crc to be corrected !!!
+ bfrag(3,nbfrag)=bfrag(1,nbfrag)
+ bfrag(4,nbfrag)=bfrag(2,nbfrag)
+crc----------------------------------------
+ endif
+ if (card(:3).eq.'END' .or. card(:3).eq.'TER') goto 10
+C Fish out the ATOM cards.
+ if (index(card(1:4),'ATOM').gt.0) then
+ read (card(14:16),'(a3)') atom
+ if (atom.eq.'CA' .or. atom.eq.'CH3') then
+C Calculate the CM of the preceding residue.
+ if (ibeg.eq.0) then
+ if (unres_pdb) then
+ do j=1,3
+ dc(j,ires+nres)=sccor(j,iii)
+ enddo
+ else
+ call sccenter(ires,iii,sccor)
+ endif
+ endif
+C Start new residue.
+ read (card(24:26),*) ires
+ read (card(18:20),'(a3)') res
+ if (ibeg.eq.1) then
+ ishift=ires-1
+ if (res.ne.'GLY' .and. res.ne. 'ACE') then
+ ishift=ishift-1
+ itype(1)=21
+ endif
+ ibeg=0
+ endif
+ ires=ires-ishift
+ if (res.eq.'ACE') then
+ ity=10
+ else
+ itype(ires)=rescode(ires,res,0)
+ endif
+ read(card(31:54),'(3f8.3)') (c(j,ires),j=1,3)
+c if(me.eq.king.or..not.out1file)
+c & write (iout,'(2i3,2x,a,3f8.3)')
+c & ires,itype(ires),res,(c(j,ires),j=1,3)
+ iii=1
+ do j=1,3
+ sccor(j,iii)=c(j,ires)
+ enddo
+ else if (atom.ne.'O '.and.atom(1:1).ne.'H' .and.
+ & atom.ne.'N ' .and. atom.ne.'C ') then
+ iii=iii+1
+ read(card(31:54),'(3f8.3)') (sccor(j,iii),j=1,3)
+ endif
+ endif
+ enddo
+ 10 if(me.eq.king.or..not.out1file)
+ & write (iout,'(a,i5)') ' Nres: ',ires
+C Calculate the CM of the last side chain.
+ if (unres_pdb) then
+ do j=1,3
+ dc(j,ires+nres)=sccor(j,iii)
+ enddo
+ else
+ call sccenter(ires,iii,sccor)
+ endif
+ nres=ires
+ nsup=nres
+ nstart_sup=1
+ if (itype(nres).ne.10) then
+ nres=nres+1
+ itype(nres)=21
+ if (unres_pdb) then
+C 2/15/2013 by Adam: corrected insertion of the last dummy residue
+ call refsys(nres-3,nres-2,nres-1,e1,e2,e3,fail)
+ if (fail) then
+ e2(1)=0.0d0
+ e2(2)=1.0d0
+ e2(3)=0.0d0
+ endif
+ do j=1,3
+ c(j,nres)=c(j,nres-1)-3.8d0*e2(j)
+ enddo
+ else
+ do j=1,3
+ dcj=c(j,nres-2)-c(j,nres-3)
+ c(j,nres)=c(j,nres-1)+dcj
+ c(j,2*nres)=c(j,nres)
+ enddo
+ endif
+ endif
+ do i=2,nres-1
+ do j=1,3
+ c(j,i+nres)=dc(j,i)
+ enddo
+ enddo
+ do j=1,3
+ c(j,nres+1)=c(j,1)
+ c(j,2*nres)=c(j,nres)
+ enddo
+ if (itype(1).eq.21) then
+ nsup=nsup-1
+ nstart_sup=2
+ if (unres_pdb) then
+C 2/15/2013 by Adam: corrected insertion of the first dummy residue
+ call refsys(2,3,4,e1,e2,e3,fail)
+ if (fail) then
+ e2(1)=0.0d0
+ e2(2)=1.0d0
+ e2(3)=0.0d0
+ endif
+ do j=1,3
+ c(j,1)=c(j,2)-3.8d0*e2(j)
+ enddo
+ else
+ do j=1,3
+ dcj=c(j,4)-c(j,3)
+ c(j,1)=c(j,2)-dcj
+ c(j,nres+1)=c(j,1)
+ enddo
+ endif
+ endif
+C Calculate internal coordinates.
+ if(me.eq.king.or..not.out1file)then
+ write (iout,'(a)')
+ & "Backbone and SC coordinates as read from the PDB"
+ do ires=1,nres
+ write (iout,'(2i3,2x,a,3f8.3,5x,3f8.3)')
+ & ires,itype(ires),restyp(itype(ires)),(c(j,ires),j=1,3),
+ & (c(j,nres+ires),j=1,3)
+ enddo
+ endif
+ call int_from_cart(.true.,.false.)
+ call sc_loc_geom(.false.)
+ do i=1,nres
+ thetaref(i)=theta(i)
+ phiref(i)=phi(i)
+ enddo
+ do i=1,nres-1
+ do j=1,3
+ dc(j,i)=c(j,i+1)-c(j,i)
+ dc_norm(j,i)=dc(j,i)*vbld_inv(i+1)
+ enddo
+ enddo
+ do i=2,nres-1
+ do j=1,3
+ dc(j,i+nres)=c(j,i+nres)-c(j,i)
+ dc_norm(j,i+nres)=dc(j,i+nres)*vbld_inv(i+nres)
+ enddo
+c write (iout,*) i,(dc(j,i+nres),j=1,3),(dc_norm(j,i+nres),j=1,3),
+c & vbld_inv(i+nres)
+ enddo
+c call chainbuild
+C Copy the coordinates to reference coordinates
+ do i=1,2*nres
+ do j=1,3
+ cref(j,i)=c(j,i)
+ enddo
+ enddo
+
+
+ do j=1,nbfrag
+ do i=1,4
+ bfrag(i,j)=bfrag(i,j)-ishift
+ enddo
+ enddo
+
+ do j=1,nhfrag
+ do i=1,2
+ hfrag(i,j)=hfrag(i,j)-ishift
+ enddo
+ enddo
+
+ return
+ end
+c---------------------------------------------------------------------------
+ subroutine int_from_cart(lside,lprn)
+ implicit real*8 (a-h,o-z)
+ include 'DIMENSIONS'
+#ifdef MPI
+ include "mpif.h"
+#endif
+ include 'COMMON.LOCAL'
+ include 'COMMON.VAR'
+ include 'COMMON.CHAIN'
+ include 'COMMON.INTERACT'
+ include 'COMMON.IOUNITS'
+ include 'COMMON.GEO'
+ include 'COMMON.NAMES'
+ include 'COMMON.CONTROL'
+ include 'COMMON.SETUP'
+ character*3 seq,atom,res
+ character*80 card
+ dimension sccor(3,20)
+ integer rescode
+ logical lside,lprn
+ if(me.eq.king.or..not.out1file)then
+ if (lprn) then
+ write (iout,'(/a)')
+ & 'Internal coordinates calculated from crystal structure.'
+ if (lside) then
+ write (iout,'(8a)') ' Res ',' dvb',' Theta',
+ & ' Gamma',' Dsc_id',' Dsc',' Alpha',
+ & ' Beta '
+ else
+ write (iout,'(4a)') ' Res ',' dvb',' Theta',
+ & ' Gamma'
+ endif
+ endif
+ endif
+ do i=1,nres-1
+ iti=itype(i)
+ if (dist(i,i+1).lt.2.0D0 .or. dist(i,i+1).gt.5.0D0) then
+ write (iout,'(a,i4)') 'Bad Cartesians for residue',i
+ctest stop
+ endif
+ vbld(i+1)=dist(i,i+1)
+ vbld_inv(i+1)=1.0d0/vbld(i+1)
+ if (i.gt.1) theta(i+1)=alpha(i-1,i,i+1)
+ if (i.gt.2) phi(i+1)=beta(i-2,i-1,i,i+1)
+ enddo
+c if (unres_pdb) then
+c if (itype(1).eq.21) then
+c theta(3)=90.0d0*deg2rad
+c phi(4)=180.0d0*deg2rad
+c vbld(2)=3.8d0
+c vbld_inv(2)=1.0d0/vbld(2)
+c endif
+c if (itype(nres).eq.21) then
+c theta(nres)=90.0d0*deg2rad
+c phi(nres)=180.0d0*deg2rad
+c vbld(nres)=3.8d0
+c vbld_inv(nres)=1.0d0/vbld(2)
+c endif
+c endif
+ if (lside) then
+ do i=2,nres-1
+ do j=1,3
+ c(j,maxres2)=0.5D0*(2*c(j,i)+(c(j,i-1)-c(j,i))*vbld_inv(i)
+ & +(c(j,i+1)-c(j,i))*vbld_inv(i+1))
+ enddo
+ iti=itype(i)
+ di=dist(i,nres+i)
+C 10/03/12 Adam: Correction for zero SC-SC bond length
+ if (itype(i).ne.10 .and. itype(i).ne.21. and. di.eq.0.0d0)
+ & di=dsc(itype(i))
+ vbld(i+nres)=di
+ if (itype(i).ne.10) then
+ vbld_inv(i+nres)=1.0d0/di
+ else
+ vbld_inv(i+nres)=0.0d0
+ endif
+ if (iti.ne.10) then
+ alph(i)=alpha(nres+i,i,maxres2)
+ omeg(i)=beta(nres+i,i,maxres2,i+1)
+ endif
+ if(me.eq.king.or..not.out1file)then
+ if (lprn)
+ & write (iout,'(a3,i4,7f10.3)') restyp(iti),i,vbld(i),
+ & rad2deg*theta(i),rad2deg*phi(i),dsc(iti),vbld(nres+i),
+ & rad2deg*alph(i),rad2deg*omeg(i)
+ endif
+ enddo
+ else if (lprn) then
+ do i=2,nres
+ iti=itype(i)
+ if(me.eq.king.or..not.out1file)
+ & write (iout,'(a3,i4,7f10.3)') restyp(iti),i,dist(i,i-1),
+ & rad2deg*theta(i),rad2deg*phi(i)
+ enddo
+ endif
+ return
+ end
+c-------------------------------------------------------------------------------
+ subroutine sc_loc_geom(lprn)
+ implicit real*8 (a-h,o-z)
+ include 'DIMENSIONS'
+#ifdef MPI
+ include "mpif.h"
+#endif
+ include 'COMMON.LOCAL'
+ include 'COMMON.VAR'
+ include 'COMMON.CHAIN'
+ include 'COMMON.INTERACT'
+ include 'COMMON.IOUNITS'
+ include 'COMMON.GEO'
+ include 'COMMON.NAMES'
+ include 'COMMON.CONTROL'
+ include 'COMMON.SETUP'
+ double precision x_prime(3),y_prime(3),z_prime(3)
+ logical lprn
+ do i=1,nres-1
+ do j=1,3
+ dc_norm(j,i)=vbld_inv(i+1)*(c(j,i+1)-c(j,i))
+ enddo
+ enddo
+ do i=2,nres-1
+ if (itype(i).ne.10) then
+ do j=1,3
+ dc_norm(j,i+nres)=vbld_inv(i+nres)*(c(j,i+nres)-c(j,i))
+ enddo
+ else
+ do j=1,3
+ dc_norm(j,i+nres)=0.0d0
+ enddo
+ endif
+ enddo
+ do i=2,nres-1
+ costtab(i+1) =dcos(theta(i+1))
+ sinttab(i+1) =dsqrt(1-costtab(i+1)*costtab(i+1))
+ cost2tab(i+1)=dsqrt(0.5d0*(1.0d0+costtab(i+1)))
+ sint2tab(i+1)=dsqrt(0.5d0*(1.0d0-costtab(i+1)))
+ cosfac2=0.5d0/(1.0d0+costtab(i+1))
+ cosfac=dsqrt(cosfac2)
+ sinfac2=0.5d0/(1.0d0-costtab(i+1))
+ sinfac=dsqrt(sinfac2)
+ it=itype(i)
+ if (it.ne.10) then
+c
+C Compute the axes of tghe local cartesian coordinates system; store in
+c x_prime, y_prime and z_prime
+c
+ do j=1,3
+ x_prime(j) = 0.00
+ y_prime(j) = 0.00
+ z_prime(j) = 0.00
+ enddo
+ do j = 1,3
+ x_prime(j) = (dc_norm(j,i) - dc_norm(j,i-1))*cosfac
+ y_prime(j) = (dc_norm(j,i) + dc_norm(j,i-1))*sinfac
+ enddo
+ call vecpr(x_prime,y_prime,z_prime)
+c
+C Transform the unit vector of the ith side-chain centroid, dC_norm(*,i),
+C to local coordinate system. Store in xx, yy, zz.
+c
+ xx=0.0d0
+ yy=0.0d0
+ zz=0.0d0
+ do j = 1,3
+ xx = xx + x_prime(j)*dc_norm(j,i+nres)
+ yy = yy + y_prime(j)*dc_norm(j,i+nres)
+ zz = zz + z_prime(j)*dc_norm(j,i+nres)
+ enddo
+
+ xxref(i)=xx
+ yyref(i)=yy
+ zzref(i)=zz
+ else
+ xxref(i)=0.0d0
+ yyref(i)=0.0d0
+ zzref(i)=0.0d0
+ endif
+ enddo
+ if (lprn) then
+ do i=2,nres
+ iti=itype(i)
+ if(me.eq.king.or..not.out1file)
+ & write (iout,'(a3,i4,3f10.5)') restyp(iti),i,xxref(i),
+ & yyref(i),zzref(i)
+ enddo
+ endif
+ return
+ end
+c---------------------------------------------------------------------------
+ subroutine sccenter(ires,nscat,sccor)
+ implicit real*8 (a-h,o-z)
+ include 'DIMENSIONS'
+ include 'COMMON.CHAIN'
+ dimension sccor(3,20)
+ do j=1,3
+ sccmj=0.0D0
+ do i=1,nscat
+ sccmj=sccmj+sccor(j,i)
+ enddo
+ dc(j,ires)=sccmj/nscat
+ enddo
+ return
+ end
+c---------------------------------------------------------------------------
+ subroutine bond_regular
+ implicit real*8 (a-h,o-z)
+ include 'DIMENSIONS'
+ include 'COMMON.VAR'
+ include 'COMMON.LOCAL'
+ include 'COMMON.CALC'
+ include 'COMMON.INTERACT'
+ include 'COMMON.CHAIN'
+ do i=1,nres-1
+ vbld(i+1)=vbl
+ vbld_inv(i+1)=1.0d0/vbld(i+1)
+ vbld(i+1+nres)=dsc(itype(i+1))
+ vbld_inv(i+1+nres)=dsc_inv(itype(i+1))
+c print *,vbld(i+1),vbld(i+1+nres)
+ enddo
+ return
+ end
projects / unres.git / blobdiff