c c c ################################################### c ## COPYRIGHT (C) 1990 by Jay William Ponder ## c ## All Rights Reserved ## c ################################################### c c ################################################################ c ## ## c ## program pdbxyz -- Protein Data Bank to XYZ coordinates ## c ## ## c ################################################################ c c c "pdbxyz" takes as input an RCSB Protein Data Bank file and then c converts to and writes out a Tinker Cartesian coordinates file, c and a sequence file for biopolymers c c program pdbxyz use atomid use atoms use couple use files use inform use katoms use pdb use resdue use sequen use titles implicit none integer i,j,it,next integer ipdb,ixyz,iseq integer last,pdbleng integer freeunit integer, allocatable :: row(:) real*8 xi,yi,zi,rij real*8 rcut,rmax(0:25) logical biopoly logical clash character*1 letter character*3 resname character*3 reslast character*240 pdbfile character*240 xyzfile character*240 seqfile character*240 pdbtitle c c c get the Protein Data Bank file and a parameter set c call initial call getpdb call field call unitcell c c save the title line from the PDB file for later use c pdbleng = ltitle pdbtitle = title(1:ltitle) c c decide whether the system has only biopolymers and water c biopoly = .false. reslast = '***' do i = 1, npdb if (pdbrec(i) .eq. 'ATOM ') then resname = pdbres(i) if (resname .ne. reslast) then reslast = resname do j = 1, maxamino if (resname .eq. amino(j)) then biopoly = .true. goto 10 end if end do do j = 1, maxnuc if (resname .eq. nuclz(j)) then biopoly = .true. goto 10 end if end do biopoly = .false. goto 20 10 continue end if else if (pdbrec(i) .eq. 'HETATM') then resname = pdbres(i) if (resname .ne. reslast) then reslast = resname if (resname.eq.'HOH' .or. resname.eq.' LI' .or. & resname.eq.' NA' .or. resname.eq.' K' .or. & resname.eq.' RB' .or. resname.eq.' CS' .or. & resname.eq.' MG' .or. resname.eq.' CA' .or. & resname.eq.' SR' .or. resname.eq.' BA' .or. & resname.eq.' F' .or. resname.eq.' CL' .or. & resname.eq.' BR' .or. resname.eq.' I' .or. & resname.eq.' ZN') then pdbrec(i) = 'HETATM' end if end if end if end do 20 continue c c open the Tinker coordinates file to be used for output c ixyz = freeunit () xyzfile = filename(1:leng)//'.xyz' call version (xyzfile,'new') open (unit=ixyz,file=xyzfile,status='new') c c reopen the PDB file and read the first coordinate set c ipdb = freeunit () pdbfile = filename call suffix (pdbfile,'pdb','old') open (unit=ipdb,file=pdbfile,status ='old') rewind (unit=ipdb) if (pdbtyp .eq. 'PDB') call readpdb (ipdb) if (pdbtyp .eq. 'CIF') call readcif (ipdb) c c use special translation mechanisms for biopolymers c do while (.not. abort) if (biopoly) then n = 0 do i = 1, nchain if (chntyp(i) .eq. 'PEPTIDE') call ribosome (i) if (chntyp(i) .eq. 'NUCLEIC') call ligase (i) end do call hetatom last = n do i = last, 1, -1 if (type(i) .eq. 0) call delete (i) end do c c get general atom properties for non-biopolymer structures c else n = npdb do i = 1, n x(i) = xpdb(i) y(i) = ypdb(i) z(i) = zpdb(i) if (pdbsym(i) .ne. ' ') then name(i) = pdbsym(i) else letter = pdbatm(i)(1:1) if (letter.ge.'A' .and. letter.le.'Z') then name(i) = pdbatm(i)(1:3) else name(i) = pdbatm(i)(2:4) end if end if n12(i) = 0 next = 1 call getnumb (pdbres(i),type(i),next) end do c c add missing hydrogen atoms to satisfy empty valences c c call addhydro c c perform dynamic allocation of some local arrays c allocate (row(n)) c c set atom size classification from periodic table row c do i = 1, n it = type(i) if (it .eq. 0) then atomic(i) = 0 letter = name(i)(1:1) call upcase (letter) if (letter .eq. 'H') then row(i) = 1 atomic(i) = 1 else if (letter .eq. 'B') then row(i) = 2 atomic(i) = 5 if (name(i)(2:2) .eq. 'R') then row(i) = 5 atomic(i) = 35 end if else if (letter .eq. 'C') then row(i) = 2 atomic(i) = 6 if (name(i)(2:2) .eq. 'L') then row(i) = 3 atomic(i) = 17 end if else if (letter .eq. 'N') then row(i) = 2 atomic(i) = 7 else if (letter .eq. 'O') then row(i) = 2 atomic(i) = 8 else if (letter .eq. 'F') then row(i) = 2 atomic(i) = 9 else if (letter .eq. 'P') then row(i) = 3 atomic(i) = 15 else if (letter .eq. 'S') then row(i) = 3 atomic(i) = 16 if (name(i)(2:2) .eq. 'I') then row(i) = 3 atomic(i) = 14 end if else if (letter .eq. 'I') then row(i) = 5 atomic(i) = 53 else row(i) = 0 end if else if (ligand(it) .eq. 0) then row(i) = 0 else if (atmnum(it) .le. 2) then row(i) = 1 else if (atmnum(it) .le. 10) then row(i) = 2 else if (atmnum(it) .le. 18) then row(i) = 3 else row(i) = 5 end if end do c c set the maximum bonded distance between atom type pairs c rmax(0) = -1.0d0 rmax(1) = -1.0d0 rmax(2) = 1.3d0 rmax(3) = 1.55d0 rmax(4) = 1.75d0 rmax(5) = 1.90d0 rmax(6) = 2.0d0 rmax(9) = 2.2d0 rmax(10) = 2.4d0 rmax(15) = 2.6d0 rmax(25) = 2.8d0 c c OpenMP directives for the major loop structure c !$OMP PARALLEL default(private) !$OMP& shared(n,x,y,z,row,rmax,n12,i12) !$OMP DO c c find and connect atom pairs within bonding distance c do i = 1, n-1 xi = x(i) yi = y(i) zi = z(i) do j = i+1, n rcut = rmax(row(i)*row(j))**2 rij = (xi-x(j))**2 + (yi-y(j))**2 + (zi-z(j))**2 if (rij .le. rcut) then n12(i) = n12(i) + 1 i12(n12(i),i) = j n12(j) = n12(j) + 1 i12(n12(j),j) = i end if end do end do c c OpenMP directives for the major loop structure c !$OMP END DO !$OMP END PARALLEL c c perform deallocation of some local arrays c deallocate (row) c c assign generic atom types if currently unassigned c do i = 1, n if (it .eq. 0) type(i) = 10*atomic(i) + n12(i) end do end if c c sort the attached atom lists into ascending order c do i = 1, n call sort8 (n12(i),i12(1,i)) end do c c check for atom pairs with identical coordinates c clash = .false. call chkxyz (clash) c c write the coordinates file and reset the connectivities c ltitle = pdbleng title = pdbtitle(1:ltitle) call prtxyz (ixyz) do i = 1, npdb n12(i) = 0 end do c c read the next coordinate set from Protein Data Bank file c if (nmodel .eq. 1) then abort = .true. else imodel = imodel + 1 rewind (unit=ipdb) if (pdbtyp .eq. 'PDB') call readpdb (ipdb) if (pdbtyp .eq. 'CIF') call readcif (ipdb) end if end do c c write a sequence file for proteins and nucleic acids c if (biopoly) then iseq = freeunit () seqfile = filename(1:leng)//'.seq' call version (seqfile,'new') open (unit=iseq,file=seqfile,status='new') call prtseq (iseq) close (unit=iseq) end if c c perform any final tasks before program exit c close (unit=ixyz) call final end c c c ################################################################# c ## ## c ## subroutine ribosome -- coordinates from PDB polypeptide ## c ## ## c ################################################################# c c c "ribosome" translates a polypeptide structure in Protein Data c Bank format to a Cartesian coordinate file and sequence file c c subroutine ribosome (ichn) use atoms use fields use files use inform use iounit use pdb use resdue use sequen implicit none integer i,j,k,m integer ichn,ityp integer jres,kres integer start,stop integer cyxtyp integer ncys,ndisulf integer, allocatable :: ni(:) integer, allocatable :: cai(:) integer, allocatable :: ci(:) integer, allocatable :: oi(:) integer, allocatable :: si(:) integer, allocatable :: icys(:) integer, allocatable :: idisulf(:,:) real*8 xr,yr,zr,r real*8, allocatable :: xcys(:) real*8, allocatable :: ycys(:) real*8, allocatable :: zcys(:) logical newchn logical midchn logical endchn logical cyclic character*3 resname character*4 atmname save si c c c perform dynamic allocation of some local arrays c allocate (ni(nres)) allocate (cai(nres)) allocate (ci(nres)) allocate (oi(nres)) allocate (si(nres)) allocate (icys(nres)) allocate (idisulf(2,nres)) allocate (xcys(nres)) allocate (ycys(nres)) allocate (zcys(nres)) c c set the next atom and the residue range of the chain c n = n + 1 jres = ichain(1,ichn) kres = ichain(2,ichn) do i = jres, kres ni(i) = 0 cai(i) = 0 ci(i) = 0 oi(i) = 0 end do c c check for the presence of a cyclic polypeptide chain c cyclic = .false. start = resatm(1,jres) stop = resatm(2,jres) call findatm (' N ',start,stop,j) if (j .ne. 0) ni(jres) = j start = resatm(1,kres) stop = resatm(2,kres) call findatm (' C ',start,stop,k) if (k .ne. 0) ci(kres) = k if (jres.ne.kres .and. j.ne.0 .and. k.ne.0) then xr = xpdb(k) - xpdb(j) yr = ypdb(k) - ypdb(j) zr = zpdb(k) - zpdb(j) r = sqrt(xr*xr + yr*yr + zr*zr) if (r .le. 3.0d0) cyclic = .true. end if c c search for any potential cystine disulfide bonds c do i = 1, maxamino if (amino(i) .eq. 'CYX') cyxtyp = i end do ncys = 0 do i = 1, nres start = resatm(1,i) resname = pdbres(start) if (resname.eq.'CYS' .or. resname.eq.'CYX') then stop = resatm(2,i) call findatm (' SG ',start,stop,k) ncys = ncys + 1 icys(ncys) = i xcys(ncys) = xpdb(k) ycys(ncys) = ypdb(k) zcys(ncys) = zpdb(k) end if end do ndisulf = 0 do i = 1, ncys-1 do k = i+1, ncys xr = xcys(k) - xcys(i) yr = ycys(k) - ycys(i) zr = zcys(k) - zcys(i) r = sqrt(xr*xr + yr*yr + zr*zr) if (r .le. 3.0d0) then ndisulf = ndisulf + 1 idisulf(1,ndisulf) = min(icys(i),icys(k)) idisulf(2,ndisulf) = max(icys(i),icys(k)) end if end do end do do i = 1, ndisulf j = idisulf(1,i) k = idisulf(2,i) seqtyp(j) = cyxtyp seqtyp(k) = cyxtyp seq(j) = 'CYX' seq(k) = 'CYX' start = resatm(1,j) stop = resatm(2,j) do m = start, stop pdbres(m) = 'CYX' end do start = resatm(1,k) stop = resatm(2,k) do m = start, stop pdbres(m) = 'CYX' end do end do c c locate and assign the atoms that make up each residue c do i = jres, kres ityp = seqtyp(i) start = resatm(1,i) stop = resatm(2,i) resname = seq(i) c c check that the maximum allowed atoms is not exceeded c if (n+25 .gt. maxatm) then write (iout,10) maxatm 10 format (/,' RIBOSOME -- The Maximum of',i9,' Atoms', & ' has been Exceeded') call fatal end if c c test location of residue within the current chain c newchn = .false. midchn = .false. endchn = .false. if (i .eq. jres) newchn = .true. if (i .eq. kres) endchn = .true. if (.not.newchn .and. .not.endchn) midchn = .true. c c build the amide nitrogen of the current residue c atmname = ' N ' if (resname .eq. 'COH') atmname = ' OH ' call findatm (atmname,start,stop,k) if (k .ne. 0) ni(i) = n if (midchn) then j = ntyp(ityp) call oldatm (k,j,ci(i-1),i) else if (newchn) then if (cyclic) then j = ntyp(ityp) else j = nntyp(ityp) end if call oldatm (k,j,0,i) else if (endchn) then if (cyclic) then j = ntyp(ityp) else j = nctyp(ityp) end if call oldatm (k,j,ci(i-1),i) end if c c build the alpha carbon of the current residue c atmname = ' CA ' if (resname .eq. 'ACE') atmname = ' CH3' if (resname .eq. 'NME') atmname = ' C ' call findatm (atmname,start,stop,k) if (k .ne. 0) cai(i) = n if (midchn .or. cyclic .or. nres.eq.1) then j = catyp(ityp) call oldatm (k,j,ni(i),i) else if (newchn) then j = cantyp(ityp) call oldatm (k,j,ni(i),i) else if (endchn) then j = cactyp(ityp) call oldatm (k,j,ni(i),i) end if c c build the carbonyl carbon of the current residue c call findatm (' C ',start,stop,k) if (k .ne. 0) ci(i) = n if (midchn .or. cyclic) then j = ctyp(ityp) call oldatm (k,j,cai(i),i) else if (newchn) then j = cntyp(ityp) call oldatm (k,j,cai(i),i) else if (endchn) then j = cctyp(ityp) if (resname .eq. 'COH') then type(ci(i-1)) = biotyp(j) else call oldatm (k,j,cai(i),i) end if end if c c build the carbonyl oxygen of the current residue c call findatm (' O ',start,stop,k) if (k .ne. 0) oi(i) = n if (midchn .or. cyclic) then j = otyp(ityp) call oldatm (k,j,ci(i),i) else if (newchn) then j = ontyp(ityp) call oldatm (k,j,ci(i),i) else if (endchn) then j = octyp(ityp) if (resname .eq. 'COH') then type(oi(i-1)) = biotyp(j) else call oldatm (k,j,ci(i),i) end if end if c c build the amide hydrogens of the current residue c if (midchn .or. (endchn.and.cyclic)) then j = hntyp(ityp) call findatm (' H ',start,stop,k) call newatm (k,j,ni(i),1.01d0,ci(i-1),119.0d0, & cai(i),119.0d0,1) else if (newchn .and. cyclic) then j = hntyp(ityp) call findatm (' H ',start,stop,k) call newatm (k,j,ni(i),1.01d0,ci(kres),119.0d0, & cai(i),119.0d0,1) else if (newchn) then j = hnntyp(ityp) if (resname .eq. 'PRO') then call findatm (' H2 ',start,stop,k) call newatm (k,j,ni(i),1.01d0,cai(i),109.5d0, & ci(i),0.0d0,0) call findatm (' H3 ',start,stop,k) call newatm (k,j,ni(i),1.01d0,cai(i),109.5d0, & ci(i),-120.0d0,0) else if (resname .eq. 'PCA') then call findatm (' H ',start,stop,k) call newatm (k,j,ni(i),1.01d0,cai(i),109.5d0, & ci(i),-60.0d0,0) else call findatm (' H1 ',start,stop,k) if (k .eq. 0) call findatm (' H ',start,stop,k) call newatm (k,j,ni(i),1.01d0,cai(i),109.5d0, & ci(i),180.0d0,0) call findatm (' H2 ',start,stop,k) call newatm (k,j,ni(i),1.01d0,cai(i),109.5d0, & ci(i),60.0d0,0) call findatm (' H3 ',start,stop,k) call newatm (k,j,ni(i),1.01d0,cai(i),109.5d0, & ci(i),-60.0d0,0) end if else if (endchn) then j = hnctyp(ityp) if (resname .eq. 'COH') then call findatm (' HO ',start,stop,k) call newatm (k,j,ni(i),0.98d0,ci(i-1),108.7d0, & cai(i-1),180.0d0,0) else if (resname .eq. 'NH2') then call findatm (' H1 ',start,stop,k) if (k .eq. 0) call findatm (' H ',start,stop,k) call newatm (k,j,ni(i),1.01d0,ci(i-1),120.9d0, & cai(i-1),0.0d0,0) call findatm (' H2 ',start,stop,k) call newatm (k,j,ni(i),1.01d0,ci(i-1),120.3d0, & cai(i-1),180.0d0,0) else if (resname .eq. 'NME') then call findatm (' H ',start,stop,k) call newatm (k,j,ni(i),1.01d0,ci(i-1),119.0d0, & cai(i),119.0d0,1) else call findatm (' H ',start,stop,k) call newatm (k,j,ni(i),1.01d0,ci(i-1),119.0d0, & cai(i),119.0d0,1) end if end if c c build the alpha hydrogen of the current residue c if (resname .eq. 'GLY') then call findatm (' HA2',start,stop,k) else call findatm (' HA ',start,stop,k) end if if (midchn .or. cyclic) then j = hatyp(ityp) call newatm (k,j,cai(i),1.10d0,ni(i),109.5d0, & ci(i),109.5d0,-1) else if (newchn) then j = hantyp(ityp) if (resname .eq. 'FOR') then call findatm (' H ',start,stop,k) call newatm (k,j,ci(i),1.12d0,oi(i),0.0d0,0,0.0d0,0) else if (resname .eq. 'ACE') then call findatm (' H1 ',start,stop,k) if (k .eq. 0) call findatm (' H ',start,stop,k) call newatm (k,j,cai(i),1.10d0,ci(i),109.5d0, & oi(i),180.0d0,0) call findatm (' H2 ',start,stop,k) call newatm (k,j,cai(i),1.10d0,ci(i),109.5d0, & oi(i),60.0d0,0) call findatm (' H3 ',start,stop,k) call newatm (k,j,cai(i),1.10d0,ci(i),109.5d0, & oi(i),-60.0d0,0) else call newatm (k,j,cai(i),1.10d0,ni(i),109.5d0, & ci(i),109.5d0,-1) end if else if (endchn) then j = hactyp(ityp) if (resname .eq. 'NME') then call findatm (' H1 ',start,stop,k) if (k .eq. 0) call findatm (' H ',start,stop,k) call newatm (k,j,cai(i),1.10d0,ni(i),109.5d0, & ci(i-1),180.0d0,0) call findatm (' H2 ',start,stop,k) call newatm (k,j,cai(i),1.10d0,ni(i),109.5d0, & ci(i-1),60.0d0,0) call findatm (' H3 ',start,stop,k) call newatm (k,j,cai(i),1.10d0,ni(i),109.5d0, & ci(i-1),-60.0d0,0) else call newatm (k,j,cai(i),1.10d0,ni(i),109.5d0, & ci(i),109.5d0,-1) end if end if c c build the side chain atoms of the current residue c call addside (resname,i,newchn,endchn,start,stop, & cai(i),ni(i),ci(i),si(i)) c c build the terminal oxygen at the end of a peptide chain c if (endchn .and. .not.cyclic .and. resname.ne.'COH') then call findatm (' OXT',start,stop,k) if (k .eq. 0) call findatm (' OT2',start,stop,k) j = octyp(ityp) call newatm (k,j,ci(i),1.25d0,cai(i),117.0d0, & oi(i),126.0d0,1) end if end do c c connect the terminal residues if the chain is cyclic c if (cyclic) then call addbond (ni(jres),ci(kres)) if (verbose) then write (iout,20) jres,kres 20 format (/,' Peptide Cyclization between Residues : ',2i5) end if end if c c connect the sulfur atoms involved in disulfide bonds c do i = 1, ndisulf j = idisulf(1,i) k = idisulf(2,i) if (k.ge.ichain(1,ichn) .and. k.le.ichain(2,ichn)) then call addbond (si(j),si(k)) if (verbose) then write (iout,30) j,k 30 format (/,' Disulfide Bond between Residues : ',2i5) end if end if end do c c total number of atoms is one less than the current atom c n = n - 1 c c perform deallocation of some local arrays c deallocate (ni) deallocate (cai) deallocate (ci) deallocate (oi) deallocate (si) deallocate (icys) deallocate (idisulf) deallocate (xcys) deallocate (ycys) deallocate (zcys) return end c c c ################################################################ c ## ## c ## subroutine addside -- build the amino acid side chains ## c ## ## c ################################################################ c c c "addside" builds the Cartesian coordinates for a single amino c acid side chain; coordinates are read from the Protein Data c Bank file or found from internal coordinates, then atom types c are assigned and connectivity data generated c c note biotypes of CD and HD atoms for N-terminal proline are c set as absolute values, not relative to the CB atom; this may c need updating if the list of biotypes changes in the future c c subroutine addside (resname,ires,newchn,endchn, & start,stop,cai,ni,ci,si) use atoms use resdue use sequen implicit none integer i,k,ires integer start,stop integer cai,ni,ci,si logical newchn,endchn character*3 resname c c c zero out disulfide and set CB atom as reference site c si = 0 k = cbtyp(seqtyp(ires)) c c glycine residue (GLY) c if (resname .eq. 'GLY') then call findatm (' HA3',start,stop,i) k = hatyp(seqtyp(ires)) if (newchn) k = hantyp(seqtyp(ires)) if (endchn) k = hactyp(seqtyp(ires)) call newatm (i,k,cai,1.10d0,ni,109.5d0,ci,109.5d0,1) c c alanine residue (ALA) c else if (resname .eq. 'ALA') then call findatm (' CB ',start,stop,i) call oldatm (i,k,cai,ires) call findatm (' HB1',start,stop,i) call newatm (i,k+1,n-1,1.10d0,cai,110.2d0,ni,180.0d0,0) call findatm (' HB2',start,stop,i) call newatm (i,k+1,n-2,1.10d0,cai,110.2d0,ni,60.0d0,0) call findatm (' HB3',start,stop,i) call newatm (i,k+1,n-3,1.10d0,cai,110.2d0,ni,-60.0d0,0) c c valine residue (VAL) c else if (resname .eq. 'VAL') then call findatm (' CB ',start,stop,i) call oldatm (i,k,cai,ires) call findatm (' CG1',start,stop,i) call oldatm (i,k+2,n-1,ires) call findatm (' CG2',start,stop,i) call oldatm (i,k+4,n-2,ires) call findatm (' HB ',start,stop,i) call newatm (i,k+1,n-3,1.10d0,cai,107.0d0,n-2,108.2d0,1) call findatm ('HG11',start,stop,i) call newatm (i,k+3,n-3,1.10d0,n-4,111.6d0,cai,180.0d0,0) call findatm ('HG12',start,stop,i) call newatm (i,k+3,n-4,1.10d0,n-5,111.6d0,cai,60.0d0,0) call findatm ('HG13',start,stop,i) call newatm (i,k+3,n-5,1.10d0,n-6,111.6d0,cai,-60.0d0,0) call findatm ('HG21',start,stop,i) call newatm (i,k+5,n-5,1.10d0,n-7,111.6d0,cai,180.0d0,0) call findatm ('HG22',start,stop,i) call newatm (i,k+5,n-6,1.10d0,n-8,111.6d0,cai,60.0d0,0) call findatm ('HG23',start,stop,i) call newatm (i,k+5,n-7,1.10d0,n-9,111.6d0,cai,-60.0d0,0) c c leucine residue (LEU) c else if (resname .eq. 'LEU') then call findatm (' CB ',start,stop,i) call oldatm (i,k,cai,ires) call findatm (' CG ',start,stop,i) call oldatm (i,k+2,n-1,ires) call findatm (' CD1',start,stop,i) call oldatm (i,k+4,n-1,ires) call findatm (' CD2',start,stop,i) call oldatm (i,k+6,n-2,ires) call findatm (' HB2',start,stop,i) call newatm (i,k+1,n-4,1.10d0,cai,107.9d0,n-3,110.0d0,1) call findatm (' HB3',start,stop,i) call newatm (i,k+1,n-5,1.10d0,cai,107.9d0,n-4,110.0d0,-1) call findatm (' HG ',start,stop,i) call newatm (i,k+3,n-5,1.10d0,n-6,107.0d0,n-4,108.2d0,1) call findatm ('HD11',start,stop,i) call newatm (i,k+5,n-5,1.10d0,n-6,111.6d0,n-7,180.0d0,0) call findatm ('HD12',start,stop,i) call newatm (i,k+5,n-6,1.10d0,n-7,111.6d0,n-8,60.0d0,0) call findatm ('HD13',start,stop,i) call newatm (i,k+5,n-7,1.10d0,n-8,111.6d0,n-9,-60.0d0,0) call findatm ('HD21',start,stop,i) call newatm (i,k+7,n-7,1.10d0,n-9,111.6d0,n-10,180.0d0,0) call findatm ('HD22',start,stop,i) call newatm (i,k+7,n-8,1.10d0,n-10,111.6d0,n-11,60.0d0,0) call findatm ('HD23',start,stop,i) call newatm (i,k+7,n-9,1.10d0,n-11,111.6d0,n-12,-60.0d0,0) c c isoleucine residue (ILE) c else if (resname .eq. 'ILE') then call findatm (' CB ',start,stop,i) call oldatm (i,k,cai,ires) call findatm (' CG1',start,stop,i) call oldatm (i,k+2,n-1,ires) call findatm (' CG2',start,stop,i) call oldatm (i,k+4,n-2,ires) call findatm (' CD1',start,stop,i) if (i .eq. 0) call findatm (' CD ',start,stop,i) call oldatm (i,k+6,n-2,ires) call findatm (' HB ',start,stop,i) call newatm (i,k+1,n-4,1.10d0,cai,107.0d0,n-3,108.2d0,-1) call findatm ('HG12',start,stop,i) call newatm (i,k+3,n-4,1.10d0,n-5,109.5d0,n-2,109.5d0,1) call findatm ('HG13',start,stop,i) call newatm (i,k+3,n-5,1.10d0,n-6,109.5d0,n-3,109.5d0,-1) call findatm ('HG21',start,stop,i) call newatm (i,k+5,n-5,1.10d0,n-7,111.6d0,cai,180.0d0,0) call findatm ('HG22',start,stop,i) call newatm (i,k+5,n-6,1.10d0,n-8,111.6d0,cai,60.0d0,0) call findatm ('HG23',start,stop,i) call newatm (i,k+5,n-7,1.10d0,n-9,111.6d0,cai,-60.0d0,0) call findatm ('HD11',start,stop,i) call newatm (i,k+7,n-7,1.10d0,n-9,111.6d0,n-10,180.0d0,0) call findatm ('HD12',start,stop,i) call newatm (i,k+7,n-8,1.10d0,n-10,111.6d0,n-11,60.0d0,0) call findatm ('HD13',start,stop,i) call newatm (i,k+7,n-9,1.10d0,n-11,111.6d0,n-12,-60.0d0,0) c c serine residue (SER) c else if (resname .eq. 'SER') then call findatm (' CB ',start,stop,i) call oldatm (i,k,cai,ires) call findatm (' OG ',start,stop,i) call oldatm (i,k+2,n-1,ires) call findatm (' HB2',start,stop,i) call newatm (i,k+1,n-2,1.10d0,cai,109.2d0,n-1,109.5d0,1) call findatm (' HB3',start,stop,i) call newatm (i,k+1,n-3,1.10d0,cai,109.2d0,n-2,109.5d0,-1) call findatm (' HG ',start,stop,i) call newatm (i,k+3,n-3,0.94d0,n-4,106.9d0,cai,180.0d0,0) c c threonine residue (THR) c else if (resname .eq. 'THR') then call findatm (' CB ',start,stop,i) call oldatm (i,k,cai,ires) call findatm (' OG1',start,stop,i) call oldatm (i,k+2,n-1,ires) call findatm (' CG2',start,stop,i) call oldatm (i,k+4,n-2,ires) call findatm (' HB ',start,stop,i) call newatm (i,k+1,n-3,1.10d0,cai,107.0d0,n-2,108.2d0,-1) call findatm (' HG1',start,stop,i) call newatm (i,k+3,n-3,0.94d0,n-4,106.9d0,cai,180.0d0,0) call findatm ('HG21',start,stop,i) call newatm (i,k+5,n-3,1.10d0,n-5,111.6d0,cai,180.0d0,0) call findatm ('HG22',start,stop,i) call newatm (i,k+5,n-4,1.10d0,n-6,111.6d0,cai,60.0d0,0) call findatm ('HG23',start,stop,i) call newatm (i,k+5,n-5,1.10d0,n-7,111.6d0,cai,-60.0d0,0) c c cysteine residue (CYS) c else if (resname .eq. 'CYS') then call findatm (' CB ',start,stop,i) call oldatm (i,k,cai,ires) call findatm (' SG ',start,stop,i) call oldatm (i,k+2,n-1,ires) call findatm (' HB2',start,stop,i) call newatm (i,k+1,n-2,1.10d0,cai,109.5d0,n-1,107.5d0,1) call findatm (' HB3',start,stop,i) call newatm (i,k+1,n-3,1.10d0,cai,109.5d0,n-2,107.5d0,-1) call findatm (' HG ',start,stop,i) call newatm (i,k+3,n-3,1.34d0,n-4,96.0d0,cai,180.0d0,0) c c cystine residue (CYX) c else if (resname .eq. 'CYX') then call findatm (' CB ',start,stop,i) call oldatm (i,k,cai,ires) call findatm (' SG ',start,stop,i) si = n call oldatm (i,k+2,n-1,ires) call findatm (' HB2',start,stop,i) call newatm (i,k+1,n-2,1.10d0,cai,109.5d0,n-1,107.5d0,1) call findatm (' HB3',start,stop,i) call newatm (i,k+1,n-3,1.10d0,cai,109.5d0,n-2,107.5d0,-1) c c deprotonated cysteine residue (CYD) c else if (resname .eq. 'CYD') then call findatm (' CB ',start,stop,i) call oldatm (i,k,cai,ires) call findatm (' SG ',start,stop,i) call oldatm (i,k+2,n-1,ires) call findatm (' HB2',start,stop,i) call newatm (i,k+1,n-2,1.10d0,cai,109.5d0,n-1,107.5d0,1) call findatm (' HB3',start,stop,i) call newatm (i,k+1,n-3,1.10d0,cai,109.5d0,n-2,107.5d0,-1) c c proline residue (PRO) c else if (resname .eq. 'PRO') then call findatm (' CB ',start,stop,i) call oldatm (i,k,cai,ires) call findatm (' CG ',start,stop,i) call oldatm (i,k+2,n-1,ires) call findatm (' CD ',start,stop,i) if (newchn) then call oldatm (i,469,n-1,ires) else call oldatm (i,k+4,n-1,ires) end if call addbond (n-1,ni) call findatm (' HB2',start,stop,i) call newatm (i,k+1,n-3,1.10d0,cai,111.2d0,n-2,111.2d0,1) call findatm (' HB3',start,stop,i) call newatm (i,k+1,n-4,1.10d0,cai,111.2d0,n-3,111.2d0,-1) call findatm (' HG2',start,stop,i) call newatm (i,k+3,n-4,1.10d0,n-5,111.2d0,n-3,111.2d0,1) call findatm (' HG3',start,stop,i) call newatm (i,k+3,n-5,1.10d0,n-6,111.2d0,n-4,111.2d0,-1) if (newchn) then call findatm (' HD2',start,stop,i) call newatm (i,470,n-5,1.10d0,n-6,111.2d0,ni,111.2d0,1) call findatm (' HD3',start,stop,i) call newatm (i,470,n-6,1.10d0,n-7,111.2d0,ni,111.2d0,-1) else call findatm (' HD2',start,stop,i) call newatm (i,k+5,n-5,1.10d0,n-6,111.2d0,ni,111.2d0,1) call findatm (' HD3',start,stop,i) call newatm (i,k+5,n-6,1.10d0,n-7,111.2d0,ni,111.2d0,-1) end if c c phenylalanine residue (PHE) c else if (resname .eq. 'PHE') then call findatm (' CB ',start,stop,i) call oldatm (i,k,cai,ires) call findatm (' CG ',start,stop,i) call oldatm (i,k+2,n-1,ires) call findatm (' CD1',start,stop,i) call oldatm (i,k+3,n-1,ires) call findatm (' CD2',start,stop,i) call oldatm (i,k+3,n-2,ires) call findatm (' CE1',start,stop,i) call oldatm (i,k+5,n-2,ires) call findatm (' CE2',start,stop,i) call oldatm (i,k+5,n-2,ires) call findatm (' CZ ',start,stop,i) call oldatm (i,k+7,n-1,ires) call addbond (n-1,n-3) call findatm (' HB2',start,stop,i) call newatm (i,k+1,n-7,1.10d0,cai,107.9d0,n-6,110.0d0,1) call findatm (' HB3',start,stop,i) call newatm (i,k+1,n-8,1.10d0,cai,107.9d0,n-7,110.0d0,-1) call findatm (' HD1',start,stop,i) call newatm (i,k+4,n-7,1.09d0,n-8,120.0d0,n-9,0.0d0,0) call findatm (' HD2',start,stop,i) call newatm (i,k+4,n-7,1.09d0,n-9,120.0d0,n-10,0.0d0,0) call findatm (' HE1',start,stop,i) call newatm (i,k+6,n-7,1.09d0,n-9,120.0d0,n-10,180.0d0,0) call findatm (' HE2',start,stop,i) call newatm (i,k+6,n-7,1.09d0,n-9,120.0d0,n-11,180.0d0,0) call findatm (' HZ ',start,stop,i) call newatm (i,k+8,n-7,1.09d0,n-8,120.0d0,n-10,180.0d0,0) c c tyrosine residue (TYR) c else if (resname .eq. 'TYR') then call findatm (' CB ',start,stop,i) call oldatm (i,k,cai,ires) call findatm (' CG ',start,stop,i) call oldatm (i,k+2,n-1,ires) call findatm (' CD1',start,stop,i) call oldatm (i,k+3,n-1,ires) call findatm (' CD2',start,stop,i) call oldatm (i,k+3,n-2,ires) call findatm (' CE1',start,stop,i) call oldatm (i,k+5,n-2,ires) call findatm (' CE2',start,stop,i) call oldatm (i,k+5,n-2,ires) call findatm (' CZ ',start,stop,i) call oldatm (i,k+7,n-1,ires) call addbond (n-1,n-3) call findatm (' OH ',start,stop,i) call oldatm (i,k+8,n-1,ires) call findatm (' HB2',start,stop,i) call newatm (i,k+1,n-8,1.10d0,cai,107.9d0,n-7,110.0d0,1) call findatm (' HB3',start,stop,i) call newatm (i,k+1,n-9,1.10d0,cai,107.9d0,n-8,110.0d0,-1) call findatm (' HD1',start,stop,i) call newatm (i,k+4,n-8,1.09d0,n-9,120.0d0,n-10,0.0d0,0) call findatm (' HD2',start,stop,i) call newatm (i,k+4,n-8,1.09d0,n-10,120.0d0,n-11,0.0d0,0) call findatm (' HE1',start,stop,i) call newatm (i,k+6,n-8,1.09d0,n-10,120.0d0,n-11,180.0d0,0) call findatm (' HE2',start,stop,i) call newatm (i,k+6,n-8,1.09d0,n-10,120.0d0,n-12,180.0d0,0) call findatm (' HH ',start,stop,i) call newatm (i,k+9,n-7,0.97d0,n-8,108.0d0,n-9,0.0d0,0) c c deprotonated tyrosine residue (TYD) c else if (resname .eq. 'TYD') then call findatm (' CB ',start,stop,i) call oldatm (i,k,cai,ires) call findatm (' CG ',start,stop,i) call oldatm (i,k+2,n-1,ires) call findatm (' CD1',start,stop,i) call oldatm (i,k+3,n-1,ires) call findatm (' CD2',start,stop,i) call oldatm (i,k+3,n-2,ires) call findatm (' CE1',start,stop,i) call oldatm (i,k+5,n-2,ires) call findatm (' CE2',start,stop,i) call oldatm (i,k+5,n-2,ires) call findatm (' CZ ',start,stop,i) call oldatm (i,k+7,n-1,ires) call addbond (n-1,n-3) call findatm (' OH ',start,stop,i) call oldatm (i,k+8,n-1,ires) call findatm (' HB2',start,stop,i) call newatm (i,k+1,n-8,1.10d0,cai,107.9d0,n-7,110.0d0,1) call findatm (' HB3',start,stop,i) call newatm (i,k+1,n-9,1.10d0,cai,107.9d0,n-8,110.0d0,-1) call findatm (' HD1',start,stop,i) call newatm (i,k+4,n-8,1.09d0,n-9,120.0d0,n-10,0.0d0,0) call findatm (' HD2',start,stop,i) call newatm (i,k+4,n-8,1.09d0,n-10,120.0d0,n-11,0.0d0,0) call findatm (' HE1',start,stop,i) call newatm (i,k+6,n-8,1.09d0,n-10,120.0d0,n-11,180.0d0,0) call findatm (' HE2',start,stop,i) call newatm (i,k+6,n-8,1.09d0,n-10,120.0d0,n-12,180.0d0,0) c c tryptophan residue (TRP) c else if (resname .eq. 'TRP') then call findatm (' CB ',start,stop,i) call oldatm (i,k,cai,ires) call findatm (' CG ',start,stop,i) call oldatm (i,k+2,n-1,ires) call findatm (' CD1',start,stop,i) call oldatm (i,k+3,n-1,ires) call findatm (' CD2',start,stop,i) call oldatm (i,k+5,n-2,ires) call findatm (' NE1',start,stop,i) call oldatm (i,k+6,n-2,ires) call findatm (' CE2',start,stop,i) call oldatm (i,k+8,n-1,ires) call addbond (n-1,n-3) call findatm (' CE3',start,stop,i) call oldatm (i,k+9,n-3,ires) call findatm (' CZ2',start,stop,i) call oldatm (i,k+11,n-2,ires) call findatm (' CZ3',start,stop,i) call oldatm (i,k+13,n-2,ires) call findatm (' CH2',start,stop,i) call oldatm (i,k+15,n-1,ires) call addbond (n-1,n-3) call findatm (' HB2',start,stop,i) call newatm (i,k+1,n-10,1.10d0,cai,107.9d0,n-9,110.0d0,1) call findatm (' HB3',start,stop,i) call newatm (i,k+1,n-11,1.10d0,cai,107.9d0,n-10,110.0d0,-1) call findatm (' HD1',start,stop,i) call newatm (i,k+4,n-10,1.09d0,n-11,126.0d0,n-12,0.0d0,0) call findatm (' HE1',start,stop,i) call newatm (i,k+7,n-9,1.01d0,n-11,126.3d0,n-12,180.0d0,0) call findatm (' HE3',start,stop,i) call newatm (i,k+10,n-8,1.09d0,n-6,120.0d0,n-5,180.0d0,0) call findatm (' HZ2',start,stop,i) call newatm (i,k+12,n-8,1.09d0,n-6,120.0d0,n-7,180.0d0,0) call findatm (' HZ3',start,stop,i) call newatm (i,k+14,n-8,1.09d0,n-7,120.0d0,n-9,180.0d0,0) call findatm (' HH2',start,stop,i) call newatm (i,k+16,n-8,1.09d0,n-9,120.0d0,n-11,180.0d0,0) c c histidine (HD and HE) residue (HIS) c else if (resname .eq. 'HIS') then call findatm (' CB ',start,stop,i) call oldatm (i,k,cai,ires) call findatm (' CG ',start,stop,i) call oldatm (i,k+2,n-1,ires) call findatm (' ND1',start,stop,i) call oldatm (i,k+3,n-1,ires) call findatm (' CD2',start,stop,i) call oldatm (i,k+5,n-2,ires) call findatm (' CE1',start,stop,i) call oldatm (i,k+7,n-2,ires) call findatm (' NE2',start,stop,i) call oldatm (i,k+9,n-1,ires) call addbond (n-1,n-3) call findatm (' HB2',start,stop,i) call newatm (i,k+1,n-6,1.10d0,cai,107.9d0,n-5,110.0d0,1) call findatm (' HB3',start,stop,i) call newatm (i,k+1,n-7,1.10d0,cai,107.9d0,n-6,110.0d0,-1) call findatm (' HD1',start,stop,i) call newatm (i,k+4,n-6,1.02d0,n-4,126.0d0,n-3,180.0d0,0) call findatm (' HD2',start,stop,i) call newatm (i,k+6,n-6,1.09d0,n-4,126.0d0,n-5,180.0d0,0) call findatm (' HE1',start,stop,i) call newatm (i,k+8,n-6,1.09d0,n-5,126.0d0,n-7,180.0d0,0) call findatm (' HE2',start,stop,i) call newatm (i,k+10,n-6,1.02d0,n-7,126.0d0,n-9,180.0d0,0) c c histidine (HD only) residue (HID) c else if (resname .eq. 'HID') then call findatm (' CB ',start,stop,i) call oldatm (i,k,cai,ires) call findatm (' CG ',start,stop,i) call oldatm (i,k+2,n-1,ires) call findatm (' ND1',start,stop,i) call oldatm (i,k+3,n-1,ires) call findatm (' CD2',start,stop,i) call oldatm (i,k+5,n-2,ires) call findatm (' CE1',start,stop,i) call oldatm (i,k+7,n-2,ires) call findatm (' NE2',start,stop,i) call oldatm (i,k+9,n-1,ires) call addbond (n-1,n-3) call findatm (' HB2',start,stop,i) call newatm (i,k+1,n-6,1.10d0,cai,107.9d0,n-5,110.0d0,1) call findatm (' HB3',start,stop,i) call newatm (i,k+1,n-7,1.10d0,cai,107.9d0,n-6,110.0d0,-1) call findatm (' HD1',start,stop,i) call newatm (i,k+4,n-6,1.02d0,n-4,126.0d0,n-3,180.0d0,0) call findatm (' HD2',start,stop,i) call newatm (i,k+6,n-6,1.09d0,n-4,126.0d0,n-5,180.0d0,0) call findatm (' HE1',start,stop,i) call newatm (i,k+8,n-6,1.09d0,n-5,126.0d0,n-7,180.0d0,0) c c histidine (HE only) residue (HIE) c else if (resname .eq. 'HIE') then call findatm (' CB ',start,stop,i) call oldatm (i,k,cai,ires) call findatm (' CG ',start,stop,i) call oldatm (i,k+2,n-1,ires) call findatm (' ND1',start,stop,i) call oldatm (i,k+3,n-1,ires) call findatm (' CD2',start,stop,i) call oldatm (i,k+4,n-2,ires) call findatm (' CE1',start,stop,i) call oldatm (i,k+6,n-2,ires) call findatm (' NE2',start,stop,i) call oldatm (i,k+8,n-1,ires) call addbond (n-1,n-3) call findatm (' HB2',start,stop,i) call newatm (i,k+1,n-6,1.10d0,cai,107.9d0,n-5,110.0d0,1) call findatm (' HB3',start,stop,i) call newatm (i,k+1,n-7,1.10d0,cai,107.9d0,n-6,110.0d0,-1) call findatm (' HD2',start,stop,i) call newatm (i,k+5,n-5,1.09d0,n-3,126.0d0,n-4,180.0d0,0) call findatm (' HE1',start,stop,i) call newatm (i,k+7,n-5,1.09d0,n-4,126.0d0,n-6,180.0d0,0) call findatm (' HE2',start,stop,i) call newatm (i,k+9,n-5,1.02d0,n-6,126.0d0,n-8,180.0d0,0) c c aspartate residue (ASP) c else if (resname .eq. 'ASP') then call findatm (' CB ',start,stop,i) call oldatm (i,k,cai,ires) call findatm (' CG ',start,stop,i) call oldatm (i,k+2,n-1,ires) call findatm (' OD1',start,stop,i) call oldatm (i,k+3,n-1,ires) call findatm (' OD2',start,stop,i) call oldatm (i,k+3,n-2,ires) call findatm (' HB2',start,stop,i) call newatm (i,k+1,n-4,1.10d0,cai,107.9d0,n-3,110.0d0,1) call findatm (' HB3',start,stop,i) call newatm (i,k+1,n-5,1.10d0,cai,107.9d0,n-4,110.0d0,-1) c c protonated aspartic acid residue (ASH) c else if (resname .eq. 'ASH') then call findatm (' CB ',start,stop,i) call oldatm (i,k,cai,ires) call findatm (' CG ',start,stop,i) call oldatm (i,k+2,n-1,ires) call findatm (' OD1',start,stop,i) call oldatm (i,k+3,n-1,ires) call findatm (' OD2',start,stop,i) call oldatm (i,k+4,n-2,ires) call findatm (' HB2',start,stop,i) call newatm (i,k+1,n-4,1.10d0,cai,107.9d0,n-3,110.0d0,1) call findatm (' HB3',start,stop,i) call newatm (i,k+1,n-5,1.10d0,cai,107.9d0,n-4,110.0d0,-1) call findatm (' HD2',start,stop,i) call newatm (i,k+5,n-3,0.98d0,n-5,108.7d0,n-4,0.0d0,0) c c asparagine residue (ASN) c else if (resname .eq. 'ASN') then call findatm (' CB ',start,stop,i) call oldatm (i,k,cai,ires) call findatm (' CG ',start,stop,i) call oldatm (i,k+2,n-1,ires) call findatm (' OD1',start,stop,i) call oldatm (i,k+3,n-1,ires) call findatm (' ND2',start,stop,i) call oldatm (i,k+4,n-2,ires) call findatm (' HB2',start,stop,i) call newatm (i,k+1,n-4,1.10d0,cai,107.9d0,n-3,110.0d0,1) call findatm (' HB3',start,stop,i) call newatm (i,k+1,n-5,1.10d0,cai,107.9d0,n-4,110.0d0,-1) call findatm ('HD21',start,stop,i) call newatm (i,k+5,n-3,1.01d0,n-5,120.9d0,n-6,0.0d0,0) call findatm ('HD22',start,stop,i) call newatm (i,k+5,n-4,1.01d0,n-6,120.3d0,n-7,180.0d0,0) c c glutamate residue (GLU) c else if (resname .eq. 'GLU') then call findatm (' CB ',start,stop,i) call oldatm (i,k,cai,ires) call findatm (' CG ',start,stop,i) call oldatm (i,k+2,n-1,ires) call findatm (' CD ',start,stop,i) call oldatm (i,k+4,n-1,ires) call findatm (' OE1',start,stop,i) call oldatm (i,k+5,n-1,ires) call findatm (' OE2',start,stop,i) call oldatm (i,k+5,n-2,ires) call findatm (' HB2',start,stop,i) call newatm (i,k+1,n-5,1.10d0,cai,107.9d0,n-4,110.0d0,1) call findatm (' HB3',start,stop,i) call newatm (i,k+1,n-6,1.10d0,cai,107.9d0,n-5,110.0d0,-1) call findatm (' HG2',start,stop,i) call newatm (i,k+3,n-6,1.10d0,n-7,109.5d0,n-5,109.5d0,1) call findatm (' HG3',start,stop,i) call newatm (i,k+3,n-7,1.10d0,n-8,109.5d0,n-6,109.5d0,-1) c c protonated glutamic acid residue (GLH) c else if (resname .eq. 'GLH') then call findatm (' CB ',start,stop,i) call oldatm (i,k,cai,ires) call findatm (' CG ',start,stop,i) call oldatm (i,k+2,n-1,ires) call findatm (' CD ',start,stop,i) call oldatm (i,k+4,n-1,ires) call findatm (' OE1',start,stop,i) call oldatm (i,k+5,n-1,ires) call findatm (' OE2',start,stop,i) call oldatm (i,k+6,n-2,ires) call findatm (' HB2',start,stop,i) call newatm (i,k+1,n-5,1.10d0,cai,107.9d0,n-4,110.0d0,1) call findatm (' HB3',start,stop,i) call newatm (i,k+1,n-6,1.10d0,cai,107.9d0,n-5,110.0d0,-1) call findatm (' HG2',start,stop,i) call newatm (i,k+3,n-6,1.10d0,n-7,109.5d0,n-5,109.5d0,1) call findatm (' HG3',start,stop,i) call newatm (i,k+3,n-7,1.10d0,n-8,109.5d0,n-6,109.5d0,-1) call findatm (' HE2',start,stop,i) call newatm (i,k+7,n-5,0.98d0,n-7,108.7d0,n-6,0.0d0,0) c c glutamine residue (GLN) c else if (resname .eq. 'GLN') then call findatm (' CB ',start,stop,i) call oldatm (i,k,cai,ires) call findatm (' CG ',start,stop,i) call oldatm (i,k+2,n-1,ires) call findatm (' CD ',start,stop,i) call oldatm (i,k+4,n-1,ires) call findatm (' OE1',start,stop,i) call oldatm (i,k+5,n-1,ires) call findatm (' NE2',start,stop,i) call oldatm (i,k+6,n-2,ires) call findatm (' HB2',start,stop,i) call newatm (i,k+1,n-5,1.10d0,cai,107.9d0,n-4,110.0d0,1) call findatm (' HB3',start,stop,i) call newatm (i,k+1,n-6,1.10d0,cai,107.9d0,n-5,110.0d0,-1) call findatm (' HG2',start,stop,i) call newatm (i,k+3,n-6,1.10d0,n-7,109.5d0,n-5,109.5d0,1) call findatm (' HG3',start,stop,i) call newatm (i,k+3,n-7,1.10d0,n-8,109.5d0,n-6,109.5d0,-1) call findatm ('HE21',start,stop,i) call newatm (i,k+7,n-5,1.01d0,n-7,120.9d0,n-8,0.0d0,0) call findatm ('HE22',start,stop,i) call newatm (i,k+7,n-6,1.01d0,n-8,120.3d0,n-9,180.0d0,0) c c methionine residue (MET) c else if (resname .eq. 'MET') then call findatm (' CB ',start,stop,i) call oldatm (i,k,cai,ires) call findatm (' CG ',start,stop,i) call oldatm (i,k+2,n-1,ires) call findatm (' SD ',start,stop,i) call oldatm (i,k+4,n-1,ires) call findatm (' CE ',start,stop,i) call oldatm (i,k+5,n-1,ires) call findatm (' HB2',start,stop,i) call newatm (i,k+1,n-4,1.10d0,cai,107.9d0,n-3,110.0d0,1) call findatm (' HB3',start,stop,i) call newatm (i,k+1,n-5,1.10d0,cai,107.9d0,n-4,110.0d0,-1) call findatm (' HG2',start,stop,i) call newatm (i,k+3,n-5,1.10d0,n-6,109.5d0,n-4,109.5d0,1) call findatm (' HG3',start,stop,i) call newatm (i,k+3,n-6,1.10d0,n-7,109.5d0,n-5,109.5d0,-1) call findatm (' HE1',start,stop,i) call newatm (i,k+6,n-5,1.10d0,n-6,110.2d0,n-7,180.0d0,0) call findatm (' HE2',start,stop,i) call newatm (i,k+6,n-6,1.10d0,n-7,110.2d0,n-8,60.0d0,0) call findatm (' HE3',start,stop,i) call newatm (i,k+6,n-7,1.10d0,n-8,110.2d0,n-9,-60.0d0,0) c c lysine residue (LYS) c else if (resname .eq. 'LYS') then call findatm (' CB ',start,stop,i) call oldatm (i,k,cai,ires) call findatm (' CG ',start,stop,i) call oldatm (i,k+2,n-1,ires) call findatm (' CD ',start,stop,i) call oldatm (i,k+4,n-1,ires) call findatm (' CE ',start,stop,i) call oldatm (i,k+6,n-1,ires) call findatm (' NZ ',start,stop,i) call oldatm (i,k+8,n-1,ires) call findatm (' HB2',start,stop,i) call newatm (i,k+1,n-5,1.10d0,cai,107.9d0,n-4,110.0d0,1) call findatm (' HB3',start,stop,i) call newatm (i,k+1,n-6,1.10d0,cai,107.9d0,n-5,110.0d0,-1) call findatm (' HG2',start,stop,i) call newatm (i,k+3,n-6,1.10d0,n-7,109.5d0,n-5,109.5d0,1) call findatm (' HG3',start,stop,i) call newatm (i,k+3,n-7,1.10d0,n-8,109.5d0,n-6,109.5d0,-1) call findatm (' HD2',start,stop,i) call newatm (i,k+5,n-7,1.10d0,n-8,109.5d0,n-6,109.5d0,1) call findatm (' HD3',start,stop,i) call newatm (i,k+5,n-8,1.10d0,n-9,109.5d0,n-7,109.5d0,-1) call findatm (' HE2',start,stop,i) call newatm (i,k+7,n-8,1.10d0,n-9,110.9d0,n-7,107.3d0,1) call findatm (' HE3',start,stop,i) call newatm (i,k+7,n-9,1.10d0,n-10,110.9d0,n-8,107.3d0,-1) call findatm (' HZ1',start,stop,i) call newatm (i,k+9,n-9,1.04d0,n-10,110.5d0,n-11,180.0d0,0) call findatm (' HZ2',start,stop,i) call newatm (i,k+9,n-10,1.04d0,n-11,110.5d0,n-12,60.0d0,0) call findatm (' HZ3',start,stop,i) call newatm (i,k+9,n-11,1.04d0,n-12,110.5d0,n-13,-60.0d0,0) c c deprotonated lysine residue (LYD) c else if (resname .eq. 'LYD') then call findatm (' CB ',start,stop,i) call oldatm (i,k,cai,ires) call findatm (' CG ',start,stop,i) call oldatm (i,k+2,n-1,ires) call findatm (' CD ',start,stop,i) call oldatm (i,k+4,n-1,ires) call findatm (' CE ',start,stop,i) call oldatm (i,k+6,n-1,ires) call findatm (' NZ ',start,stop,i) call oldatm (i,k+8,n-1,ires) call findatm (' HB2',start,stop,i) call newatm (i,k+1,n-5,1.10d0,cai,107.9d0,n-4,110.0d0,1) call findatm (' HB3',start,stop,i) call newatm (i,k+1,n-6,1.10d0,cai,107.9d0,n-5,110.0d0,-1) call findatm (' HG2',start,stop,i) call newatm (i,k+3,n-6,1.10d0,n-7,109.5d0,n-5,109.5d0,1) call findatm (' HG3',start,stop,i) call newatm (i,k+3,n-7,1.10d0,n-8,109.5d0,n-6,109.5d0,-1) call findatm (' HD2',start,stop,i) call newatm (i,k+5,n-7,1.10d0,n-8,109.5d0,n-6,109.5d0,1) call findatm (' HD3',start,stop,i) call newatm (i,k+5,n-8,1.10d0,n-9,109.5d0,n-7,109.5d0,-1) call findatm (' HE2',start,stop,i) call newatm (i,k+7,n-8,1.10d0,n-9,110.9d0,n-7,107.3d0,1) call findatm (' HE3',start,stop,i) call newatm (i,k+7,n-9,1.10d0,n-10,110.9d0,n-8,107.3d0,-1) call findatm (' HZ1',start,stop,i) call newatm (i,k+9,n-9,1.04d0,n-10,110.5d0,n-11,180.0d0,0) call findatm (' HZ2',start,stop,i) call newatm (i,k+9,n-10,1.04d0,n-11,110.5d0,n-12,60.0d0,0) c c arginine residue (ARG) c else if (resname .eq. 'ARG') then call findatm (' CB ',start,stop,i) call oldatm (i,k,cai,ires) call findatm (' CG ',start,stop,i) call oldatm (i,k+2,n-1,ires) call findatm (' CD ',start,stop,i) call oldatm (i,k+4,n-1,ires) call findatm (' NE ',start,stop,i) call oldatm (i,k+6,n-1,ires) call findatm (' CZ ',start,stop,i) call oldatm (i,k+8,n-1,ires) call findatm (' NH1',start,stop,i) call oldatm (i,k+9,n-1,ires) call findatm (' NH2',start,stop,i) call oldatm (i,k+9,n-2,ires) call findatm (' HB2',start,stop,i) call newatm (i,k+1,n-7,1.10d0,cai,107.9d0,n-6,110.0d0,1) call findatm (' HB3',start,stop,i) call newatm (i,k+1,n-8,1.10d0,cai,107.9d0,n-7,110.0d0,-1) call findatm (' HG2',start,stop,i) call newatm (i,k+3,n-8,1.10d0,n-9,109.5d0,n-7,109.5d0,1) call findatm (' HG3',start,stop,i) call newatm (i,k+3,n-9,1.10d0,n-10,109.5d0,n-8,109.5d0,-1) call findatm (' HD2',start,stop,i) call newatm (i,k+5,n-9,1.10d0,n-10,109.5d0,n-8,109.5d0,1) call findatm (' HD3',start,stop,i) call newatm (i,k+5,n-10,1.10d0,n-11,109.5d0,n-9,109.5d0,-1) call findatm (' HE ',start,stop,i) call newatm (i,k+7,n-10,1.01d0,n-11,118.5d0,n-9,120.0d0,1) call findatm ('HH11',start,stop,i) call newatm (i,k+10,n-9,1.01d0,n-10,122.5d0,n-11,0.0d0,0) call findatm ('HH12',start,stop,i) call newatm (i,k+10,n-10,1.01d0,n-11,118.8d0,n-12,180.0d0,0) call findatm ('HH21',start,stop,i) call newatm (i,k+10,n-10,1.01d0,n-12,122.5d0,n-13,0.0d0,0) call findatm ('HH22',start,stop,i) call newatm (i,k+10,n-11,1.01d0,n-13,118.8d0,n-14,180.0d0,0) c c ornithine residue (ORN) c else if (resname .eq. 'ORN') then call findatm (' CB ',start,stop,i) call oldatm (i,k,cai,ires) call findatm (' CG ',start,stop,i) call oldatm (i,k+2,n-1,ires) call findatm (' CD ',start,stop,i) call oldatm (i,k+4,n-1,ires) call findatm (' NE ',start,stop,i) call oldatm (i,k+6,n-1,ires) call findatm (' HB2',start,stop,i) call newatm (i,k+1,n-4,1.10d0,cai,107.9d0,n-3,110.0d0,1) call findatm (' HB3',start,stop,i) call newatm (i,k+1,n-5,1.10d0,cai,107.9d0,n-4,110.0d0,-1) call findatm (' HG2',start,stop,i) call newatm (i,k+3,n-5,1.10d0,n-7,109.5d0,n-4,109.5d0,1) call findatm (' HG3',start,stop,i) call newatm (i,k+3,n-6,1.10d0,n-8,109.5d0,n-5,109.5d0,-1) call findatm (' HD2',start,stop,i) call newatm (i,k+5,n-6,1.10d0,n-8,109.5d0,n-5,109.5d0,1) call findatm (' HD3',start,stop,i) call newatm (i,k+5,n-7,1.10d0,n-9,109.5d0,n-6,109.5d0,-1) call findatm (' HE1',start,stop,i) call newatm (i,k+7,n-7,1.04d0,n-8,110.5d0,n-9,180.0d0,0) call findatm (' HE2',start,stop,i) call newatm (i,k+7,n-8,1.04d0,n-9,110.5d0,n-10,60.0d0,0) call findatm (' HE3',start,stop,i) call newatm (i,k+7,n-9,1.04d0,n-10,110.5d0,n-11,-60.0d0,0) c c methylalanine residue (AIB) c else if (resname .eq. 'AIB') then call findatm (' CB1',start,stop,i) call oldatm (i,k,cai,ires) call findatm (' CB2',start,stop,i) call oldatm (i,k,cai,ires) call findatm ('HB11',start,stop,i) call newatm (i,k+1,n-2,1.10d0,cai,110.2d0,ni,180.0d0,0) call findatm ('HB12',start,stop,i) call newatm (i,k+1,n-3,1.10d0,cai,110.2d0,ni,60.0d0,0) call findatm ('HB13',start,stop,i) call newatm (i,k+1,n-4,1.10d0,cai,110.2d0,ni,-60.0d0,0) call findatm ('HB21',start,stop,i) call newatm (i,k+1,n-4,1.10d0,cai,110.2d0,ni,180.0d0,0) call findatm ('HB22',start,stop,i) call newatm (i,k+1,n-5,1.10d0,cai,110.2d0,ni,60.0d0,0) call findatm ('HB23',start,stop,i) call newatm (i,k+1,n-6,1.10d0,cai,110.2d0,ni,-60.0d0,0) c c pyroglutamic acid residue (PCA) c else if (resname .eq. 'PCA') then call findatm (' CB ',start,stop,i) call oldatm (i,k,cai,ires) call findatm (' CG ',start,stop,i) call oldatm (i,k+2,n-1,ires) call findatm (' CD ',start,stop,i) call oldatm (i,k+4,n-1,ires) call addbond (n-1,ni) call findatm (' OE ',start,stop,i) call oldatm (i,k+5,n-1,ires) call findatm (' HB2',start,stop,i) call newatm (i,k+1,n-4,1.10d0,cai,111.2d0,n-3,111.2d0,1) call findatm (' HB3',start,stop,i) call newatm (i,k+1,n-5,1.10d0,cai,111.2d0,n-4,111.2d0,-1) call findatm (' HG2',start,stop,i) call newatm (i,k+3,n-5,1.10d0,n-6,111.2d0,n-4,111.2d0,1) call findatm (' HG3',start,stop,i) call newatm (i,k+3,n-6,1.10d0,n-7,111.2d0,n-5,111.2d0,-1) c c unknown residue (UNK) c else if (resname .eq. 'UNK') then k = hatyp(seqtyp(ires)) if (newchn) k = hantyp(seqtyp(ires)) if (endchn) k = hactyp(seqtyp(ires)) call newatm (i,k,cai,1.10d0,ni,109.5d0,ci,109.5d0,1) end if return end c c c ################################################################ c ## ## c ## subroutine ligase -- coordinates from PDB nucleic acid ## c ## ## c ################################################################ c c c "ligase" translates a nucleic acid structure in Protein Data c Bank format to a Cartesian coordinate file and sequence file c c subroutine ligase (ichn) use atoms use files use iounit use pdb use resdue use sequen implicit none integer i,j,k integer ichn,ityp integer jres,kres integer start,stop integer poi,o5i,c5i integer c4i,o4i,c1i integer c3i,c2i,o3i,o2i logical newchn,endchn logical, allocatable :: deoxy(:) character*3 resname c c c set the next atom and the residue range of the chain c n = n + 1 jres = ichain(1,ichn) kres = ichain(2,ichn) c c perform dynamic allocation of some local arrays c allocate (deoxy(nres)) c c check for deoxyribose and change residue name if necessary c do i = jres, kres deoxy(i) = .false. start = resatm(1,i) stop = resatm(2,i) resname = pdbres(start) call findatm (' O2''',start,stop,k) if (k .eq. 0) then deoxy(i) = .true. do j = start, stop if (resname .eq. ' A') pdbres(j) = ' DA' if (resname .eq. ' G') pdbres(j) = ' DG' if (resname .eq. ' C') pdbres(j) = ' DC' if (resname .eq. ' U') pdbres(j) = ' DU' if (resname .eq. ' T') pdbres(j) = ' DT' end do end if end do c c locate and assign the atoms that make up each residue c do i = jres, kres ityp = seqtyp(i) start = resatm(1,i) stop = resatm(2,i) resname = pdbres(start) c c check that the maximum allowed atoms is not exceeded c if (n+25 .gt. maxatm) then write (iout,10) maxatm 10 format (/,' LIGASE -- The Maximum of',i9,' Atoms', & ' has been Exceeded') call fatal end if c c test for initial or final residue of a nucleotide chain c newchn = .false. endchn = .false. do j = 1, nchain if (i .eq. ichain(1,j)) then newchn = .true. poi = 0 o3i = 0 end if if (i .eq. ichain(2,j)) endchn = .true. end do c c build the phosphate atoms of the current residue c if (resname .eq. ' TP') then else if (resname .eq. ' DP') then else if (resname .eq. ' MP') then else if (.not. newchn) then call findatm (' P ',start,stop,k) if (k .ne. 0) poi = n j = ptyp(ityp) call oldatm (k,j,o3i,i) call findatm (' OP1',start,stop,k) j = optyp(ityp) call oldatm (k,j,n-1,i) call findatm (' OP2',start,stop,k) j = optyp(ityp) call oldatm (k,j,n-2,i) end if c c build the ribose sugar atoms of the current residue c call findatm (' O5''',start,stop,k) if (k .ne. 0) o5i = n j = o5typ(ityp) if (newchn) then if (deoxy(i)) then j = 1244 else j = 1232 end if end if call oldatm (k,j,poi,i) call findatm (' C5''',start,stop,k) if (k .ne. 0) c5i = n j = c5typ(ityp) call oldatm (k,j,n-1,i) call findatm (' C4''',start,stop,k) if (k .ne. 0) c4i = n j = c4typ(ityp) call oldatm (k,j,n-1,i) call findatm (' O4''',start,stop,k) if (k .ne. 0) o4i = n j = o4typ(ityp) call oldatm (k,j,n-1,i) call findatm (' C1''',start,stop,k) if (k .ne. 0) c1i = n j = c1typ(ityp) call oldatm (k,j,n-1,i) call findatm (' C3''',start,stop,k) if (k .ne. 0) c3i = n j = c3typ(ityp) call oldatm (k,j,n-3,i) call findatm (' C2''',start,stop,k) if (k .ne. 0) c2i = n j = c2typ(ityp) call oldatm (k,j,n-1,i) call addbond (n-1,n-3) call findatm (' O3''',start,stop,k) if (k .ne. 0) o3i = n j = o3typ(ityp) if (endchn) then if (deoxy(i)) then j = 1249 else j = 1237 end if end if call oldatm (k,j,n-2,i) if (.not. deoxy(i)) then call findatm (' O2''',start,stop,k) if (k .ne. 0) o2i = n j = o2typ(ityp) call oldatm (k,j,n-2,i) end if c c build the hydrogen atoms of the current residue c if (newchn) then call findatm ('HO5''',start,stop,k) j = h5ttyp(ityp) call newatm (k,j,o5i,1.00d0,c5i,109.5d0,c4i,180.0d0,0) end if call findatm (' H5''',start,stop,k) j = h51typ(ityp) call newatm (k,j,c5i,1.09d0,o5i,109.5d0,c4i,109.5d0,1) call findatm ('H5''''',start,stop,k) j = h52typ(ityp) call newatm (k,j,c5i,1.09d0,o5i,109.5d0,c4i,109.5d0,-1) call findatm (' H4''',start,stop,k) j = h4typ(ityp) call newatm (k,j,c4i,1.09d0,c5i,109.5d0,c3i,109.5d0,-1) call findatm (' H3''',start,stop,k) j = h3typ(ityp) call newatm (k,j,c3i,1.09d0,c4i,109.5d0,c2i,109.5d0,-1) if (deoxy(i)) then call findatm (' H2''',start,stop,k) j = h21typ(ityp) call newatm (k,j,c2i,1.09d0,c3i,109.5d0,c1i,109.5d0,-1) call findatm ('H2''''',start,stop,k) j = h22typ(ityp) call newatm (k,j,c2i,1.09d0,c3i,109.5d0,c1i,109.5d0,1) else call findatm (' H2''',start,stop,k) j = h21typ(ityp) call newatm (k,j,c2i,1.09d0,c3i,109.5d0,c1i,109.5d0,-1) call findatm ('HO2''',start,stop,k) j = h22typ(ityp) call newatm (k,j,o2i,1.00d0,c2i,109.5d0,c3i,180.0d0,0) end if call findatm (' H1''',start,stop,k) j = h1typ(ityp) call newatm (k,j,c1i,1.09d0,o4i,109.5d0,c2i,109.5d0,-1) if (endchn) then call findatm ('HO3''',start,stop,k) j = h3ttyp(ityp) call newatm (k,j,o3i,1.00d0,c3i,109.5d0,c4i,180.0d0,0) end if c c build the standard base atoms of the current residue c call addbase (resname,i,start,stop,c1i) end do c c total number of atoms is one less than the current atom c n = n - 1 c c perform deallocation of some local arrays c deallocate (deoxy) return end c c c ################################################################ c ## ## c ## subroutine addbase -- build a single nucleic acid base ## c ## ## c ################################################################ c c c "addbase" builds the Cartesian coordinates for a single nucleic c acid base; coordinates are read from the Protein Data Bank file c or found from internal coordinates, then atom types are assigned c and connectivity data generated c c subroutine addbase (resname,ires,start,stop,c1i) use atoms implicit none integer i,ires integer start,stop integer c1i character*3 resname c c c adenine in adenosine residue (A) c if (resname .eq. ' A') then call findatm (' N9 ',start,stop,i) call oldatm (i,1017,c1i,ires) call findatm (' C8 ',start,stop,i) call oldatm (i,1021,n-1,ires) call findatm (' N7 ',start,stop,i) call oldatm (i,1020,n-1,ires) call findatm (' C5 ',start,stop,i) call oldatm (i,1019,n-1,ires) call findatm (' C6 ',start,stop,i) call oldatm (i,1025,n-1,ires) call findatm (' N6 ',start,stop,i) call oldatm (i,1027,n-1,ires) call findatm (' N1 ',start,stop,i) call oldatm (i,1024,n-2,ires) call findatm (' C2 ',start,stop,i) call oldatm (i,1023,n-1,ires) call findatm (' N3 ',start,stop,i) call oldatm (i,1022,n-1,ires) call findatm (' C4 ',start,stop,i) call oldatm (i,1018,n-1,ires) call addbond (n-1,n-7) call addbond (n-1,n-10) call findatm (' H8 ',start,stop,i) call newatm (i,1030,n-9,1.08d0,n-8,123.1d0,n-7,180.0d0,0) call findatm (' H61',start,stop,i) call newatm (i,1028,n-6,1.00d0,n-7,120.0d0,n-8,180.0d0,0) call findatm (' H62',start,stop,i) call newatm (i,1029,n-7,1.00d0,n-8,120.0d0,n-9,0.0d0,0) call findatm (' H2 ',start,stop,i) call newatm (i,1026,n-6,1.08d0,n-5,115.4d0,n-4,180.0d0,0) c c guanine in guanosine residue (G) c else if (resname .eq. ' G') then call findatm (' N9 ',start,stop,i) call oldatm (i,1047,c1i,ires) call findatm (' C8 ',start,stop,i) call oldatm (i,1051,n-1,ires) call findatm (' N7 ',start,stop,i) call oldatm (i,1050,n-1,ires) call findatm (' C5 ',start,stop,i) call oldatm (i,1049,n-1,ires) call findatm (' C6 ',start,stop,i) call oldatm (i,1055,n-1,ires) call findatm (' O6 ',start,stop,i) call oldatm (i,1060,n-1,ires) call findatm (' N1 ',start,stop,i) call oldatm (i,1054,n-2,ires) call findatm (' C2 ',start,stop,i) call oldatm (i,1053,n-1,ires) call findatm (' N2 ',start,stop,i) call oldatm (i,1057,n-1,ires) call findatm (' N3 ',start,stop,i) call oldatm (i,1052,n-2,ires) call findatm (' C4 ',start,stop,i) call oldatm (i,1048,n-1,ires) call addbond (n-1,n-8) call addbond (n-1,n-11) call findatm (' H8 ',start,stop,i) call newatm (i,1061,n-10,1.08d0,n-9,123.0d0,n-8,180.0d0,0) call findatm (' H1 ',start,stop,i) call newatm (i,1056,n-6,1.00d0,n-8,117.4d0,n-9,180.0d0,0) call findatm (' H21',start,stop,i) call newatm (i,1058,n-5,1.00d0,n-6,120.0d0,n-7,0.0d0,0) call findatm (' H22',start,stop,i) call newatm (i,1059,n-6,1.00d0,n-7,120.0d0,n-8,180.0d0,0) c c cytosine in cytidine residue (C) c else if (resname .eq. ' C') then call findatm (' N1 ',start,stop,i) call oldatm (i,1078,c1i,ires) call findatm (' C2 ',start,stop,i) call oldatm (i,1079,n-1,ires) call findatm (' O2 ',start,stop,i) call oldatm (i,1084,n-1,ires) call findatm (' N3 ',start,stop,i) call oldatm (i,1080,n-2,ires) call findatm (' C4 ',start,stop,i) call oldatm (i,1081,n-1,ires) call findatm (' N4 ',start,stop,i) call oldatm (i,1085,n-1,ires) call findatm (' C5 ',start,stop,i) call oldatm (i,1082,n-2,ires) call findatm (' C6 ',start,stop,i) call oldatm (i,1083,n-1,ires) call addbond (n-1,n-8) call findatm (' H41',start,stop,i) call newatm (i,1086,n-3,1.00d0,n-4,120.0d0,n-5,0.0d0,0) call findatm (' H42',start,stop,i) call newatm (i,1087,n-4,1.00d0,n-5,120.0d0,n-6,180.0d0,0) call findatm (' H5 ',start,stop,i) call newatm (i,1088,n-4,1.08d0,n-6,121.6d0,n-7,180.0d0,0) call findatm (' H6 ',start,stop,i) call newatm (i,1089,n-4,1.08d0,n-5,119.4d0,n-7,180.0d0,0) c c uracil in uridine residue (U) c else if (resname .eq. ' U') then call findatm (' N1 ',start,stop,i) call oldatm (i,1106,c1i,ires) call findatm (' C2 ',start,stop,i) call oldatm (i,1107,n-1,ires) call findatm (' O2 ',start,stop,i) call oldatm (i,1112,n-1,ires) call findatm (' N3 ',start,stop,i) call oldatm (i,1108,n-2,ires) call findatm (' C4 ',start,stop,i) call oldatm (i,1109,n-1,ires) call findatm (' O4 ',start,stop,i) call oldatm (i,1114,n-1,ires) call findatm (' C5 ',start,stop,i) call oldatm (i,1110,n-2,ires) call findatm (' C6 ',start,stop,i) call oldatm (i,1111,n-1,ires) call addbond (n-1,n-8) call findatm (' H3 ',start,stop,i) call newatm (i,1113,n-5,1.00d0,n-7,116.5d0,n-8,180.0d0,0) call findatm (' H5 ',start,stop,i) call newatm (i,1115,n-3,1.08d0,n-5,120.4d0,n-6,180.0d0,0) call findatm (' H6 ',start,stop,i) call newatm (i,1116,n-3,1.08d0,n-4,118.6d0,n-6,180.0d0,0) c c adenine in deoxyadenosine residue (DA) c else if (resname .eq. ' DA') then call findatm (' N9 ',start,stop,i) call oldatm (i,1132,c1i,ires) call findatm (' C8 ',start,stop,i) call oldatm (i,1136,n-1,ires) call findatm (' N7 ',start,stop,i) call oldatm (i,1135,n-1,ires) call findatm (' C5 ',start,stop,i) call oldatm (i,1134,n-1,ires) call findatm (' C6 ',start,stop,i) call oldatm (i,1140,n-1,ires) call findatm (' N6 ',start,stop,i) call oldatm (i,1142,n-1,ires) call findatm (' N1 ',start,stop,i) call oldatm (i,1139,n-2,ires) call findatm (' C2 ',start,stop,i) call oldatm (i,1138,n-1,ires) call findatm (' N3 ',start,stop,i) call oldatm (i,1137,n-1,ires) call findatm (' C4 ',start,stop,i) call oldatm (i,1133,n-1,ires) call addbond (n-1,n-7) call addbond (n-1,n-10) call findatm (' H8 ',start,stop,i) call newatm (i,1145,n-9,1.08d0,n-8,123.1d0,n-7,180.0d0,0) call findatm (' H61',start,stop,i) call newatm (i,1143,n-6,1.00d0,n-7,120.0d0,n-8,180.0d0,0) call findatm (' H62',start,stop,i) call newatm (i,1144,n-7,1.00d0,n-8,120.0d0,n-9,0.0d0,0) call findatm (' H2 ',start,stop,i) call newatm (i,1141,n-6,1.08d0,n-5,115.4d0,n-4,180.0d0,0) c c guanine in deoxyguanosine residue (DG) c else if (resname .eq. ' DG') then call findatm (' N9 ',start,stop,i) call oldatm (i,1161,c1i,ires) call findatm (' C8 ',start,stop,i) call oldatm (i,1165,n-1,ires) call findatm (' N7 ',start,stop,i) call oldatm (i,1164,n-1,ires) call findatm (' C5 ',start,stop,i) call oldatm (i,1163,n-1,ires) call findatm (' C6 ',start,stop,i) call oldatm (i,1169,n-1,ires) call findatm (' O6 ',start,stop,i) call oldatm (i,1174,n-1,ires) call findatm (' N1 ',start,stop,i) call oldatm (i,1168,n-2,ires) call findatm (' C2 ',start,stop,i) call oldatm (i,1167,n-1,ires) call findatm (' N2 ',start,stop,i) call oldatm (i,1171,n-1,ires) call findatm (' N3 ',start,stop,i) call oldatm (i,1166,n-2,ires) call findatm (' C4 ',start,stop,i) call oldatm (i,1162,n-1,ires) call addbond (n-1,n-8) call addbond (n-1,n-11) call findatm (' H8 ',start,stop,i) call newatm (i,1175,n-10,1.08d0,n-9,123.0d0,n-8,180.0d0,0) call findatm (' H1 ',start,stop,i) call newatm (i,1170,n-6,1.00d0,n-8,117.4d0,n-9,180.0d0,0) call findatm (' H21',start,stop,i) call newatm (i,1172,n-5,1.00d0,n-6,120.0d0,n-7,0.0d0,0) call findatm (' H22',start,stop,i) call newatm (i,1173,n-6,1.00d0,n-7,120.0d0,n-8,180.0d0,0) c c cytosine in deoxycytidine residue (DC) c else if (resname .eq. ' DC') then call findatm (' N1 ',start,stop,i) call oldatm (i,1191,c1i,ires) call findatm (' C2 ',start,stop,i) call oldatm (i,1192,n-1,ires) call findatm (' O2 ',start,stop,i) call oldatm (i,1197,n-1,ires) call findatm (' N3 ',start,stop,i) call oldatm (i,1193,n-2,ires) call findatm (' C4 ',start,stop,i) call oldatm (i,1194,n-1,ires) call findatm (' N4 ',start,stop,i) call oldatm (i,1198,n-1,ires) call findatm (' C5 ',start,stop,i) call oldatm (i,1195,n-2,ires) call findatm (' C6 ',start,stop,i) call oldatm (i,1196,n-1,ires) call addbond (n-1,n-8) call findatm (' H41',start,stop,i) call newatm (i,1199,n-3,1.00d0,n-4,120.0d0,n-5,0.0d0,0) call findatm (' H42',start,stop,i) call newatm (i,1200,n-4,1.00d0,n-5,120.0d0,n-6,180.0d0,0) call findatm (' H5 ',start,stop,i) call newatm (i,1201,n-4,1.08d0,n-6,121.6d0,n-7,180.0d0,0) call findatm (' H6 ',start,stop,i) call newatm (i,1202,n-4,1.08d0,n-5,119.4d0,n-7,180.0d0,0) c c thymine in deoxythymidine residue (DT) c else if (resname .eq. ' DT') then call findatm (' N1 ',start,stop,i) call oldatm (i,1218,c1i,ires) call findatm (' C2 ',start,stop,i) call oldatm (i,1219,n-1,ires) call findatm (' O2 ',start,stop,i) call oldatm (i,1224,n-1,ires) call findatm (' N3 ',start,stop,i) call oldatm (i,1220,n-2,ires) call findatm (' C4 ',start,stop,i) call oldatm (i,1221,n-1,ires) call findatm (' O4 ',start,stop,i) call oldatm (i,1226,n-1,ires) call findatm (' C5 ',start,stop,i) call oldatm (i,1222,n-2,ires) call findatm (' C7 ',start,stop,i) call oldatm (i,1227,n-1,ires) call findatm (' C6 ',start,stop,i) call oldatm (i,1223,n-2,ires) call addbond (n-1,n-9) call findatm (' H3 ',start,stop,i) call newatm (i,1225,n-6,1.00d0,n-8,116.8d0,n-9,180.0d0,0) call findatm (' H71',start,stop,i) call newatm (i,1228,n-3,1.09d0,n-4,109.5d0,n-6,0.0d0,0) call findatm (' H72',start,stop,i) call newatm (i,1228,n-4,1.09d0,n-5,109.5d0,n-1,109.5d0,1) call findatm (' H73',start,stop,i) call newatm (i,1228,n-5,1.09d0,n-6,109.5d0,n-2,109.5d0,-1) call findatm (' H6 ',start,stop,i) call newatm (i,1229,n-5,1.08d0,n-7,119.4d0,n-9,180.0d0,0) end if return end c c c ################################################################# c ## ## c ## subroutine hetatom -- coordinates of PDB water and ions ## c ## ## c ################################################################# c c c "hetatom" translates water molecules and ions in Protein Data c Bank format to a Cartesian coordinate file and sequence file c c subroutine hetatom use atoms use pdb implicit none integer i c c c find water molecules and ions in PDB HETATM records c n = n + 1 i = 0 do while (i .lt. npdb) i = i + 1 if (pdbrec(i) .eq. 'HETATM') then if (pdbres(i) .eq. 'HOH') then if (pdbatm(i) .eq. ' O ') then call oldatm (i,2001,0,0) if (pdbatm(i+1).eq.' H ' .and. & pdbatm(i+2).eq.' H ') then call oldatm (i+1,2002,n-1,0) call oldatm (i+2,2002,n-2,0) i = i + 2 if (pdbatm(i+1) .eq. ' EP ') then call oldatm (i+1,2003,n-3,0) i = i + 1 if (pdbatm(i+1) .eq. ' EP ') then call oldatm (i+1,2003,n-4,0) i = i + 1 end if end if else call newatm (0,2002,n-1,0.96d0,n-2,109.5d0, & n-3,120.0d0,0) call newatm (0,2002,n-2,0.96d0,n-1,109.5d0, & n-3,120.0d0,0) end if end if else if (pdbres(i) .eq. ' LI') then call oldatm (i,2004,0,0) else if (pdbres(i) .eq. ' NA') then call oldatm (i,2005,0,0) else if (pdbres(i) .eq. ' K') then call oldatm (i,2006,0,0) else if (pdbres(i) .eq. ' RB') then call oldatm (i,2007,0,0) else if (pdbres(i) .eq. ' CS') then call oldatm (i,2008,0,0) else if (pdbres(i) .eq. ' MG') then call oldatm (i,2009,0,0) else if (pdbres(i) .eq. ' CA') then call oldatm (i,2010,0,0) else if (pdbres(i) .eq. ' SR') then call oldatm (i,2011,0,0) else if (pdbres(i) .eq. ' BA') then call oldatm (i,2012,0,0) else if (pdbres(i) .eq. ' F') then call oldatm (i,2013,0,0) else if (pdbres(i) .eq. ' CL') then call oldatm (i,2014,0,0) else if (pdbres(i) .eq. ' BR') then call oldatm (i,2015,0,0) else if (pdbres(i) .eq. ' I') then call oldatm (i,2016,0,0) else if (pdbres(i) .eq. ' ZN') then call oldatm (i,2017,0,0) end if end if end do n = n - 1 return end c c c ############################################################ c ## ## c ## subroutine oldatm -- transfer coordinates from PDB ## c ## ## c ############################################################ c c c "oldatm" get the Cartesian coordinates for an atom from c the Protein Data Bank file, then assigns the atom type c and atomic connectivities c c subroutine oldatm (i,bionum,i1,ires) use atomid use atoms use fields use iounit use katoms use pdb use sequen implicit none integer i,bionum integer i1,ires c c c get coordinates, assign atom type, and update connectivities c if (bionum .ne. 0) then if (i .ne. 0) then type(n) = biotyp(bionum) if (type(n) .gt. 0) then name(n) = symbol(type(n)) else type(n) = 0 name(n) = ' ' end if x(n) = xpdb(i) y(n) = ypdb(i) z(n) = zpdb(i) if (i1 .ne. 0) call addbond (n,i1) n = n + 1 else write (iout,10) bionum,ires,seq(ires) 10 format (/,' OLDATM -- A PDB Atom of Biotype',i5, & ' is Missing in Residue',i5,'-',a3) call fatal end if end if return end c c c ########################################################### c ## ## c ## subroutine newatm -- create and define a new atom ## c ## ## c ########################################################### c c c "newatm" creates and defines an atom needed for the c Cartesian coordinates file, but which may not present c in the original Protein Data Bank file c c subroutine newatm (i,bionum,ia,bond,ib,angle1,ic,angle2,chiral) use atomid use atoms use fields use katoms use pdb implicit none integer i,bionum integer ia,ib,ic integer chiral real*8 bond real*8 angle1 real*8 angle2 c c c set the atom type, compute coordinates, assign c connectivities and increment the atom counter c if (bionum .ne. 0) then type(n) = biotyp(bionum) if (type(n) .gt. 0) then name(n) = symbol(type(n)) else type(n) = 0 name(n) = ' ' end if if (i .eq. 0) then call xyzatm (n,ia,bond,ib,angle1,ic,angle2,chiral) else x(n) = xpdb(i) y(n) = ypdb(i) z(n) = zpdb(i) end if call addbond (n,ia) n = n + 1 end if return end c c c ############################################################ c ## ## c ## subroutine addbond -- add a bond between two atoms ## c ## ## c ############################################################ c c c "addbond" adds entries to the attached atoms list in c order to generate a direct connection between two atoms c c subroutine addbond (i,j) use couple implicit none integer i,j c c c add connectivity between the two atoms c if (i.ne.0 .and. j.ne.0) then n12(i) = n12(i) + 1 i12(n12(i),i) = j n12(j) = n12(j) + 1 i12(n12(j),j) = i end if return end c c c ############################################################ c ## ## c ## subroutine findatm -- locate PDB atom in a residue ## c ## ## c ############################################################ c c c "findatm" locates a specific PDB atom name type within a c range of atoms from the PDB file, returns zero if the name c type was not found c c subroutine findatm (name,start,stop,ipdb) use pdb implicit none integer i,ipdb integer start,stop character*4 name c c c search for the specified atom within the residue c ipdb = 0 do i = start, stop if (pdbatm(i) .eq. name) then ipdb = i goto 10 end if end do 10 continue return end