--- /dev/null
+ subroutine elecont(lprint,ncont,icont)
+ implicit real*8 (a-h,o-z)
+ include 'DIMENSIONS'
+ include 'COMMON.IOUNITS'
+ include 'COMMON.CHAIN'
+ include 'COMMON.INTERACT'
+ include 'COMMON.LOCAL'
+ include 'COMMON.FFIELD'
+ include 'COMMON.NAMES'
+ logical lprint
+ double precision elpp_6(2,2),elpp_3(2,2),ael6_(2,2),ael3_(2,2)
+ double precision app_(2,2),bpp_(2,2),rpp_(2,2)
+ integer ncont,icont(2,maxcont)
+ double precision econt(maxcont)
+*
+* Load the constants of peptide bond - peptide bond interactions.
+* Type 1 - ordinary peptide bond, type 2 - alkylated peptide bond (e.g.
+* proline) - determined by averaging ECEPP energy.
+*
+* as of 7/06/91.
+*
+c data epp / 0.3045d0, 0.3649d0, 0.3649d0, 0.5743d0/
+ data rpp_ / 4.5088d0, 4.5395d0, 4.5395d0, 4.4846d0/
+ data elpp_6 /-0.2379d0,-0.2056d0,-0.2056d0,-0.0610d0/
+ data elpp_3 / 0.0503d0, 0.0000d0, 0.0000d0, 0.0692d0/
+ data elcutoff /-0.3d0/,elecutoff_14 /-0.5d0/
+ if (lprint) write (iout,'(a)')
+ & "Constants of electrostatic interaction energy expression."
+ do i=1,2
+ do j=1,2
+ rri=rpp_(i,j)**6
+ app_(i,j)=epp(i,j)*rri*rri
+ bpp_(i,j)=-2.0*epp(i,j)*rri
+ ael6_(i,j)=elpp_6(i,j)*4.2**6
+ ael3_(i,j)=elpp_3(i,j)*4.2**3
+ if (lprint)
+ & write (iout,'(2i2,4e15.4)') i,j,app_(i,j),bpp_(i,j),ael6_(i,j),
+ & ael3_(i,j)
+ enddo
+ enddo
+ ncont=0
+ ees=0.0
+ evdw=0.0
+ do 1 i=nnt,nct-2
+ xi=c(1,i)
+ yi=c(2,i)
+ zi=c(3,i)
+ dxi=c(1,i+1)-c(1,i)
+ dyi=c(2,i+1)-c(2,i)
+ dzi=c(3,i+1)-c(3,i)
+ xmedi=xi+0.5*dxi
+ ymedi=yi+0.5*dyi
+ zmedi=zi+0.5*dzi
+ do 4 j=i+2,nct-1
+ ind=ind+1
+ iteli=itel(i)
+ itelj=itel(j)
+ if (j.eq.i+2 .and. itelj.eq.2) iteli=2
+ if (iteli.eq.2 .and. itelj.eq.2) goto 4
+ aaa=app_(iteli,itelj)
+ bbb=bpp_(iteli,itelj)
+ ael6_i=ael6_(iteli,itelj)
+ ael3_i=ael3_(iteli,itelj)
+ dxj=c(1,j+1)-c(1,j)
+ dyj=c(2,j+1)-c(2,j)
+ dzj=c(3,j+1)-c(3,j)
+ xj=c(1,j)+0.5*dxj-xmedi
+ yj=c(2,j)+0.5*dyj-ymedi
+ zj=c(3,j)+0.5*dzj-zmedi
+ rrmij=1.0/(xj*xj+yj*yj+zj*zj)
+ rmij=sqrt(rrmij)
+ r3ij=rrmij*rmij
+ r6ij=r3ij*r3ij
+ vrmij=vblinv*rmij
+ cosa=(dxi*dxj+dyi*dyj+dzi*dzj)*vblinv2
+ cosb=(xj*dxi+yj*dyi+zj*dzi)*vrmij
+ cosg=(xj*dxj+yj*dyj+zj*dzj)*vrmij
+ fac=cosa-3.0*cosb*cosg
+ ev1=aaa*r6ij*r6ij
+ ev2=bbb*r6ij
+ fac3=ael6_i*r6ij
+ fac4=ael3_i*r3ij
+ evdwij=ev1+ev2
+ el1=fac3*(4.0+fac*fac-3.0*(cosb*cosb+cosg*cosg))
+ el2=fac4*fac
+ eesij=el1+el2
+ if (j.gt.i+2 .and. eesij.le.elcutoff .or.
+ & j.eq.i+2 .and. eesij.le.elecutoff_14) then
+ ncont=ncont+1
+ icont(1,ncont)=i
+ icont(2,ncont)=j
+ econt(ncont)=eesij
+ endif
+ ees=ees+eesij
+ evdw=evdw+evdwij
+ 4 continue
+ 1 continue
+ if (lprint) then
+ write (iout,*) 'Total average electrostatic energy: ',ees
+ write (iout,*) 'VDW energy between peptide-group centers: ',evdw
+ write (iout,*)
+ write (iout,*) 'Electrostatic contacts before pruning: '
+ do i=1,ncont
+ i1=icont(1,i)
+ i2=icont(2,i)
+ it1=itype(i1)
+ it2=itype(i2)
+ write (iout,'(i3,2x,a,i4,2x,a,i4,f10.5)')
+ & i,restyp(it1),i1,restyp(it2),i2,econt(i)
+ enddo
+ endif
+c For given residues keep only the contacts with the greatest energy.
+ i=0
+ do while (i.lt.ncont)
+ i=i+1
+ ene=econt(i)
+ ic1=icont(1,i)
+ ic2=icont(2,i)
+ j=i
+ do while (j.lt.ncont)
+ j=j+1
+ if (ic1.eq.icont(1,j).and.iabs(icont(2,j)-ic2).le.2 .or.
+ & ic2.eq.icont(2,j).and.iabs(icont(1,j)-ic1).le.2) then
+c write (iout,*) "i",i," j",j," ic1",ic1," ic2",ic2,
+c & " jc1",icont(1,j)," jc2",icont(2,j)," ncont",ncont
+ if (econt(j).lt.ene .and. icont(2,j).ne.icont(1,j)+2) then
+ if (ic1.eq.icont(1,j)) then
+ do k=1,ncont
+ if (k.ne.i .and. k.ne.j .and. icont(2,k).eq.icont(2,j)
+ & .and. iabs(icont(1,k)-ic1).le.2 .and.
+ & econt(k).lt.econt(j) ) goto 21
+ enddo
+ else if (ic2.eq.icont(2,j) ) then
+ do k=1,ncont
+ if (k.ne.i .and. k.ne.j .and. icont(1,k).eq.icont(1,j)
+ & .and. iabs(icont(2,k)-ic2).le.2 .and.
+ & econt(k).lt.econt(j) ) goto 21
+ enddo
+ endif
+c Remove ith contact
+ do k=i+1,ncont
+ icont(1,k-1)=icont(1,k)
+ icont(2,k-1)=icont(2,k)
+ econt(k-1)=econt(k)
+ enddo
+ i=i-1
+ ncont=ncont-1
+c write (iout,*) "ncont",ncont
+c do k=1,ncont
+c write (iout,*) icont(1,k),icont(2,k)
+c enddo
+ goto 20
+ else if (econt(j).gt.ene .and. ic2.ne.ic1+2)
+ & then
+ if (ic1.eq.icont(1,j)) then
+ do k=1,ncont
+ if (k.ne.i .and. k.ne.j .and. icont(2,k).eq.ic2
+ & .and. iabs(icont(1,k)-icont(1,j)).le.2 .and.
+ & econt(k).lt.econt(i) ) goto 21
+ enddo
+ else if (ic2.eq.icont(2,j) ) then
+ do k=1,ncont
+ if (k.ne.i .and. k.ne.j .and. icont(1,k).eq.ic1
+ & .and. iabs(icont(2,k)-icont(2,j)).le.2 .and.
+ & econt(k).lt.econt(i) ) goto 21
+ enddo
+ endif
+c Remove jth contact
+ do k=j+1,ncont
+ icont(1,k-1)=icont(1,k)
+ icont(2,k-1)=icont(2,k)
+ econt(k-1)=econt(k)
+ enddo
+ ncont=ncont-1
+c write (iout,*) "ncont",ncont
+c do k=1,ncont
+c write (iout,*) icont(1,k),icont(2,k)
+c enddo
+ j=j-1
+ endif
+ endif
+ 21 continue
+ enddo
+ 20 continue
+ enddo
+ if (lprint) then
+ write (iout,*)
+ write (iout,*) 'Electrostatic contacts after pruning: '
+ do i=1,ncont
+ i1=icont(1,i)
+ i2=icont(2,i)
+ it1=itype(i1)
+ it2=itype(i2)
+ write (iout,'(i3,2x,a,i4,2x,a,i4,f10.5)')
+ & i,restyp(it1),i1,restyp(it2),i2,econt(i)
+ enddo
+ endif
+ return
+ end
+c--------------------------------------------
+ subroutine secondary2(lprint)
+ implicit real*8 (a-h,o-z)
+ include 'DIMENSIONS'
+ include 'COMMON.CHAIN'
+ include 'COMMON.IOUNITS'
+ include 'COMMON.DISTFIT'
+ include 'COMMON.VAR'
+ include 'COMMON.GEO'
+ include 'COMMON.CONTROL'
+ integer ncont,icont(2,maxcont),isec(maxres,4),nsec(maxres)
+ logical lprint,not_done,freeres
+ double precision p1,p2
+ external freeres
+
+ if(.not.dccart) call chainbuild
+cd call write_pdb(99,'sec structure',0d0)
+ ncont=0
+ nbfrag=0
+ nhfrag=0
+ do i=1,nres
+ isec(i,1)=0
+ isec(i,2)=0
+ nsec(i)=0
+ enddo
+
+ call elecont(lprint,ncont,icont)
+
+c finding parallel beta
+cd write (iout,*) '------- looking for parallel beta -----------'
+ nbeta=0
+ nstrand=0
+ do i=1,ncont
+ i1=icont(1,i)
+ j1=icont(2,i)
+ if(j1-i1.gt.5 .and. freeres(i1,j1,nsec,isec)) then
+ ii1=i1
+ jj1=j1
+cd write (iout,*) i1,j1
+ not_done=.true.
+ do while (not_done)
+ i1=i1+1
+ j1=j1+1
+ do j=1,ncont
+ if (i1.eq.icont(1,j) .and. j1.eq.icont(2,j) .and.
+ & freeres(i1,j1,nsec,isec)) goto 5
+ enddo
+ not_done=.false.
+ 5 continue
+cd write (iout,*) i1,j1,not_done
+ enddo
+ j1=j1-1
+ i1=i1-1
+ if (i1-ii1.gt.1) then
+ ii1=max0(ii1-1,1)
+ jj1=max0(jj1-1,1)
+ nbeta=nbeta+1
+ if(lprint)write(iout,'(a,i3,4i4)')'parallel beta',
+ & nbeta,ii1,i1,jj1,j1
+
+ nbfrag=nbfrag+1
+ bfrag(1,nbfrag)=ii1+1
+ bfrag(2,nbfrag)=i1+1
+ bfrag(3,nbfrag)=jj1+1
+ bfrag(4,nbfrag)=min0(j1+1,nres)
+
+ do ij=ii1,i1
+ nsec(ij)=nsec(ij)+1
+ isec(ij,nsec(ij))=nbeta
+ enddo
+ do ij=jj1,j1
+ nsec(ij)=nsec(ij)+1
+ isec(ij,nsec(ij))=nbeta
+ enddo
+
+ if(lprint) then
+ nstrand=nstrand+1
+ if (nbeta.le.9) then
+ write(12,'(a18,i1,a9,i3,a2,i3,a1)')
+ & "DefPropRes 'strand",nstrand,
+ & "' 'num = ",ii1-1,"..",i1-1,"'"
+ else
+ write(12,'(a18,i2,a9,i3,a2,i3,a1)')
+ & "DefPropRes 'strand",nstrand,
+ & "' 'num = ",ii1-1,"..",i1-1,"'"
+ endif
+ nstrand=nstrand+1
+ if (nbeta.le.9) then
+ write(12,'(a18,i1,a9,i3,a2,i3,a1)')
+ & "DefPropRes 'strand",nstrand,
+ & "' 'num = ",jj1-1,"..",j1-1,"'"
+ else
+ write(12,'(a18,i2,a9,i3,a2,i3,a1)')
+ & "DefPropRes 'strand",nstrand,
+ & "' 'num = ",jj1-1,"..",j1-1,"'"
+ endif
+ write(12,'(a8,4i4)')
+ & "SetNeigh",ii1-1,i1-1,jj1-1,j1-1
+ endif
+ endif
+ endif
+ enddo
+
+c finding alpha or 310 helix
+
+ nhelix=0
+ do i=1,ncont
+ i1=icont(1,i)
+ j1=icont(2,i)
+ p1=phi(i1+2)*rad2deg
+ p2=0.0
+ if (j1+2.le.nres) p2=phi(j1+2)*rad2deg
+
+
+ if (j1.eq.i1+3 .and.
+ & ((p1.ge.10.and.p1.le.80).or.i1.le.2).and.
+ & ((p2.ge.10.and.p2.le.80).or.j1.le.2.or.j1.ge.nres-3) )then
+cd if (j1.eq.i1+3) write (iout,*) "found 1-4 ",i1,j1,p1,p2
+co if (j1.eq.i1+4) write (iout,*) "found 1-5 ",i1,j1,p1,p2
+ ii1=i1
+ jj1=j1
+ if (nsec(ii1).eq.0) then
+ not_done=.true.
+ else
+ not_done=.false.
+ endif
+ do while (not_done)
+ i1=i1+1
+ j1=j1+1
+ do j=1,ncont
+ if (i1.eq.icont(1,j) .and. j1.eq.icont(2,j)) goto 10
+ enddo
+ not_done=.false.
+ 10 continue
+ p1=phi(i1+2)*rad2deg
+ p2=phi(j1+2)*rad2deg
+ if (p1.lt.10.or.p1.gt.80.or.p2.lt.10.or.p2.gt.80)
+ & not_done=.false.
+cd write (iout,*) i1,j1,not_done,p1,p2
+ enddo
+ j1=j1+1
+ if (j1-ii1.gt.5) then
+ nhelix=nhelix+1
+cd write (iout,*)'helix',nhelix,ii1,j1
+
+ nhfrag=nhfrag+1
+ hfrag(1,nhfrag)=ii1
+ hfrag(2,nhfrag)=j1
+
+ do ij=ii1,j1
+ nsec(ij)=-1
+ enddo
+ if (lprint) then
+ write (iout,'(a,i3,2i4)') "Helix",nhelix,ii1-1,j1-1
+ if (nhelix.le.9) then
+ write(12,'(a17,i1,a9,i3,a2,i3,a1)')
+ & "DefPropRes 'helix",nhelix,
+ & "' 'num = ",ii1-1,"..",j1-2,"'"
+ else
+ write(12,'(a17,i2,a9,i3,a2,i3,a1)')
+ & "DefPropRes 'helix",nhelix,
+ & "' 'num = ",ii1-1,"..",j1-2,"'"
+ endif
+ endif
+ endif
+ endif
+ enddo
+
+ if (nhelix.gt.0.and.lprint) then
+ write(12,'(a26,$)') "DefPropRes 'helix' 'helix1"
+ do i=2,nhelix
+ if (nhelix.le.9) then
+ write(12,'(a8,i1,$)') " | helix",i
+ else
+ write(12,'(a8,i2,$)') " | helix",i
+ endif
+ enddo
+ write(12,'(a1)') "'"
+ endif
+
+
+c finding antiparallel beta
+cd write (iout,*) '--------- looking for antiparallel beta ---------'
+
+ do i=1,ncont
+ i1=icont(1,i)
+ j1=icont(2,i)
+ if (freeres(i1,j1,nsec,isec)) then
+ ii1=i1
+ jj1=j1
+cd write (iout,*) i1,j1
+
+ not_done=.true.
+ do while (not_done)
+ i1=i1+1
+ j1=j1-1
+ do j=1,ncont
+ if (i1.eq.icont(1,j).and.j1.eq.icont(2,j) .and.
+ & freeres(i1,j1,nsec,isec)) goto 6
+ enddo
+ not_done=.false.
+ 6 continue
+cd write (iout,*) i1,j1,not_done
+ enddo
+ i1=i1-1
+ j1=j1+1
+ if (i1-ii1.gt.1) then
+
+ nbfrag=nbfrag+1
+ bfrag(1,nbfrag)=ii1
+ bfrag(2,nbfrag)=min0(i1+1,nres)
+ bfrag(3,nbfrag)=min0(jj1+1,nres)
+ bfrag(4,nbfrag)=j1
+
+ nbeta=nbeta+1
+ iii1=max0(ii1-1,1)
+ do ij=iii1,i1
+ nsec(ij)=nsec(ij)+1
+ if (nsec(ij).le.2) then
+ isec(ij,nsec(ij))=nbeta
+ endif
+ enddo
+ jjj1=max0(j1-1,1)
+ do ij=jjj1,jj1
+ nsec(ij)=nsec(ij)+1
+ if (nsec(ij).le.2 .and. nsec(ij).gt.0) then
+ isec(ij,nsec(ij))=nbeta
+ endif
+ enddo
+
+
+ if (lprint) then
+ write (iout,'(a,i3,4i4)')'antiparallel beta',
+ & nbeta,ii1-1,i1,jj1,j1-1
+ nstrand=nstrand+1
+ if (nstrand.le.9) then
+ write(12,'(a18,i1,a9,i3,a2,i3,a1)')
+ & "DefPropRes 'strand",nstrand,
+ & "' 'num = ",ii1-2,"..",i1-1,"'"
+ else
+ write(12,'(a18,i2,a9,i3,a2,i3,a1)')
+ & "DefPropRes 'strand",nstrand,
+ & "' 'num = ",ii1-2,"..",i1-1,"'"
+ endif
+ nstrand=nstrand+1
+ if (nstrand.le.9) then
+ write(12,'(a18,i1,a9,i3,a2,i3,a1)')
+ & "DefPropRes 'strand",nstrand,
+ & "' 'num = ",j1-2,"..",jj1-1,"'"
+ else
+ write(12,'(a18,i2,a9,i3,a2,i3,a1)')
+ & "DefPropRes 'strand",nstrand,
+ & "' 'num = ",j1-2,"..",jj1-1,"'"
+ endif
+ write(12,'(a8,4i4)')
+ & "SetNeigh",ii1-2,i1-1,jj1-1,j1-2
+ endif
+ endif
+ endif
+ enddo
+
+ if (nstrand.gt.0.and.lprint) then
+ write(12,'(a27,$)') "DefPropRes 'sheet' 'strand1"
+ do i=2,nstrand
+ if (i.le.9) then
+ write(12,'(a9,i1,$)') " | strand",i
+ else
+ write(12,'(a9,i2,$)') " | strand",i
+ endif
+ enddo
+ write(12,'(a1)') "'"
+ endif
+
+
+
+ if (lprint) then
+ write(12,'(a37)') "DefPropRes 'coil' '! (helix | sheet)'"
+ write(12,'(a20)') "XMacStand ribbon.mac"
+
+
+ write(iout,*) 'UNRES seq:'
+ do j=1,nbfrag
+ write(iout,*) 'beta ',(bfrag(i,j),i=1,4)
+ enddo
+
+ do j=1,nhfrag
+ write(iout,*) 'helix ',(hfrag(i,j),i=1,2)
+ enddo
+ endif
+
+ return
+ end
+c-------------------------------------------------
+ logical function freeres(i,j,nsec,isec)
+ implicit real*8 (a-h,o-z)
+ include 'DIMENSIONS'
+ integer isec(maxres,4),nsec(maxres)
+ freeres=.false.
+
+ if (nsec(i).lt.0.or.nsec(j).lt.0) return
+ if (nsec(i).gt.1.or.nsec(j).gt.1) return
+ do k=1,nsec(i)
+ do l=1,nsec(j)
+ if (isec(i,k).eq.isec(j,l)) return
+ enddo
+ enddo
+ freeres=.true.
+ return
+ end
+
projects / unres.git / blobdiff