c c c ################################################### c ## COPYRIGHT (C) 1990 by Jay William Ponder ## c ## All Rights Reserved ## c ################################################### c c ############################################################### c ## ## c ## subroutine readpdb -- input of Protein Data Bank file ## c ## ## c ############################################################### c c c "readpdb" gets a set of coordinates in RCSB legacy PDB c format from an external file c c subroutine readpdb (ipdb) use boxes use files use inform use iounit use pdb use resdue use sequen use titles implicit none integer i,j,k,ipdb integer start,stop integer index,serial integer next,nxtlast integer residue,reslast integer model integer trimtext real*8 xx,yy,zz real*8 xbx,ybx,zbx real*8 aan,ban,gan logical exist,opened logical first character*1 chain,chnlast character*1 altloc character*1 insert,inslast character*1 letter character*1, allocatable :: chnatm(:) character*3 resname,atmsymb character*3 namelast character*4 atmname character*6 remark character*240 pdbfile character*240 record character*240 string save first data first / .true. / c c c open the input file if it has not already been done c inquire (unit=ipdb,opened=opened) if (.not. opened) then pdbfile = filename(1:leng)//'.pdb' call version (pdbfile,'old') inquire (file=pdbfile,exist=exist) if (exist) then open (unit=ipdb,file=pdbfile,status='old') rewind (unit=ipdb) else write (iout,10) 10 format (/,' READPDB -- Unable to Find the Protein', & ' Data Bank File') call fatal end if end if c c get alternate sites, chains and insertions to be used c if (first) call scanpdb (ipdb) c c initialize title, atom and residue counters and name c title = ' ' ltitle = 0 npdb = 0 nres = 0 reslast = maxres namelast = ' ' chnlast = ' ' model = 0 c c perform dynamic allocation of some local arrays c allocate (chnatm(maxatm)) c c perform dynamic allocation of some global arrays c if (first) then first = .false. if (.not. allocated(resnum)) allocate (resnum(maxatm)) if (.not. allocated(resatm)) allocate (resatm(2,maxatm)) if (.not. allocated(pdbmod)) allocate (pdbmod(maxatm)) if (.not. allocated(xpdb)) allocate (xpdb(maxatm)) if (.not. allocated(ypdb)) allocate (ypdb(maxatm)) if (.not. allocated(zpdb)) allocate (zpdb(maxatm)) if (.not. allocated(pdbres)) allocate (pdbres(maxatm)) if (.not. allocated(pdbsym)) allocate (pdbsym(maxatm)) if (.not. allocated(pdbatm)) allocate (pdbatm(maxatm)) if (.not. allocated(pdbrec)) allocate (pdbrec(maxatm)) end if c c process info and individual atoms from the PDB file c do while (.true.) read (ipdb,20,err=230,end=230) record 20 format (a240) remark = record(1:6) call upcase (remark) if (remark .eq. 'TITLE ') then title = record(11:70) ltitle = trimtext (title) else if (remark .eq. 'HEADER') then if (ltitle .eq. 0) then title = record(11:70) ltitle = trimtext (title) end if else if (remark .eq. 'CRYST1') then next = 7 string = record(next:240) read (string,*) xbx,ybx,zbx,aan,ban,gan if (xbx .gt. 1.0d0) then xbox = xbx ybox = ybx zbox = zbx alpha = aan beta = ban gamma = gan call unitcell end if else if (remark .eq. 'ATOM ') then next = 7 call getnumb (record,serial,next) string = record(next+1:next+4) read (string,30) atmname 30 format (a4) call upcase (atmname) string = record(next+5:next+5) read (string,40) altloc 40 format (a1) string = record(next+6:next+8) read (string,50) resname 50 format (a3) call upcase (resname) string = record(next+10:next+10) read (string,60) chain 60 format (a1) next = next + 11 nxtlast = next call getnumb (record,residue,next) if (next .eq. nxtlast) then string = record(next:next+3) read (string,70) residue 70 format (i4) next = next + 4 end if string = record(next:next) read (string,80) insert 80 format (a1) string = record(next+1:240) read (string,*,err=90,end=90) xx,yy,zz goto 100 90 continue string = record(31:38) read (string,*) xx string = record(39:46) read (string,*) yy string = record(47:54) read (string,*) zz 100 continue next = 77 call getword (record,atmsymb,next) if (index(chnsym,chain) .eq. 0) goto 120 if (altloc.ne.' ' .and. altloc.ne.altsym) goto 120 if (insert.ne.' ' .and. index(instyp,insert).eq.0) goto 120 if (model.ne.imodel .and. imodel.ne.0) goto 120 call fixpdb (resname,atmname) if (resname .eq. 'HOH') then remark = 'HETATM' else if (resname .eq. ' LI') then remark = 'HETATM' else if (resname .eq. ' F') then remark = 'HETATM' else if (resname .eq. ' NA') then remark = 'HETATM' else if (resname .eq. ' MG') then remark = 'HETATM' else if (resname .eq. ' CL') then remark = 'HETATM' else if (resname .eq. ' K') then remark = 'HETATM' else if (resname .eq. ' CA') then remark = 'HETATM' else if (resname .eq. ' FE') then remark = 'HETATM' else if (resname .eq. ' ZN') then remark = 'HETATM' else if (resname .eq. ' BR') then remark = 'HETATM' else if (resname .eq. ' I') then remark = 'HETATM' else if (residue.ne.reslast .or. resname.ne.namelast .or. & chain.ne.chnlast .or. insert.ne.inslast) then nres = nres + 1 reslast = residue namelast = resname chnlast = chain inslast = insert if (nres .gt. maxres) then write (iout,110) maxres 110 format (/,' READPDB -- The Maximum of',i6, & ' Residues has been Exceeded') call fatal end if nseq = nres seq(nseq) = resname end if npdb = npdb + 1 xpdb(npdb) = xx ypdb(npdb) = yy zpdb(npdb) = zz pdbrec(npdb) = remark pdbatm(npdb) = atmname pdbsym(npdb) = atmsymb pdbres(npdb) = resname pdbmod(npdb) = model resnum(npdb) = nres if (resname .eq. 'HOH') resnum(npdb) = 0 chnatm(npdb) = chain 120 continue else if (remark .eq. 'HETATM') then next = 7 call getnumb (record,serial,next) string = record(next+1:next+4) read (string,130) atmname 130 format (a4) call upcase (atmname) string = record(next+5:next+5) read (string,140) altloc 140 format (a1) string = record(next+6:next+8) read (string,150) resname 150 format (a3) call upcase (resname) string = record(next+10:next+10) read (string,160) chain 160 format (a1) next = next + 11 call getnumb (record,residue,next) if (next .eq. nxtlast) then string = record(next:next+3) read (string,170) residue 170 format (i4) next = next + 4 end if string = record(next:next) read (string,180) insert 180 format (a1) string = record(next+1:240) read (string,*,err=190,end=190) xx,yy,zz goto 200 190 continue string = record(31:38) read (string,*) xx string = record(39:46) read (string,*) yy string = record(47:54) read (string,*) zz 200 continue next = 77 call getword (record,atmsymb,next) if (index(chnsym,chain) .eq. 0) goto 210 if (altloc.ne.' ' .and. altloc.ne.altsym) goto 210 if (insert.ne.' ' .and. index(instyp,insert).eq.0) goto 210 if (model.ne.imodel .and. imodel.ne.0) goto 210 call fixpdb (resname,atmname) npdb = npdb + 1 xpdb(npdb) = xx ypdb(npdb) = yy zpdb(npdb) = zz pdbrec(npdb) = remark pdbatm(npdb) = atmname pdbsym(npdb) = atmsymb pdbres(npdb) = resname pdbmod(npdb) = model resnum(npdb) = 0 chnatm(npdb) = chain 210 continue else if (remark .eq. 'MODEL ') then next = 7 string = record(next:240) read (string,*) model else if (remark .eq. 'END ') then goto 230 end if if (npdb .gt. maxatm) then write (iout,220) maxatm 220 format (/,' READPDB -- The Maximum of',i6, & ' Atoms has been Exceeded') call fatal end if end do 230 continue c c set the total sequence length and chain terminus sites c if (npdb .ne. 0) then nchain = 0 chnlast = '#' do i = 1, npdb if (pdbrec(i) .eq. 'ATOM ') then letter = chnatm(i) if (letter .ne. chnlast) then nchain = nchain + 1 ichain(1,nchain) = resnum(i) chnnam(nchain) = letter chnlast = letter else ichain(2,nchain) = resnum(i) end if end if end do end if c c perform deallocation of some local arrays c deallocate (chnatm) c c find the type of species present in each chain c do i = 1, nchain start = ichain(1,i) stop = ichain(2,i) chntyp(i) = 'GENERIC' do j = start, stop do k = 1, maxamino if (seq(j) .eq. amino(k)) then chntyp(i) = 'PEPTIDE' goto 240 end if end do chntyp(i) = 'GENERIC' goto 250 240 continue end do 250 continue if (chntyp(i) .eq. 'GENERIC') then do j = start, stop do k = 1, maxnuc if (seq(j) .eq. nuclz(k)) then chntyp(i) = 'NUCLEIC' goto 260 end if end do chntyp(i) = 'GENERIC' goto 270 260 continue end do 270 continue end if end do c c get the three-letter sequence and code for each residue c do i = 1, nchain start = ichain(1,i) stop = ichain(2,i) do j = start, stop do k = 1, maxamino if (seq(j) .eq. amino(k)) then seqtyp(j) = k goto 280 end if end do do k = 1, maxnuc if (seq(j) .eq. nuclz(k)) then seqtyp(j) = k goto 280 end if end do seq(j) = 'UNK' seqtyp(j) = 0 if (chntyp(i) .eq. 'PEPTIDE') seqtyp(j) = maxamino if (chntyp(i) .eq. 'NUCLEIC') seqtyp(j) = maxnuc 280 continue end do end do c c set a pointer to the first and last atom of each residue c nres = 0 k = 0 do i = 1, npdb if (pdbrec(i) .eq. 'ATOM ') then if (resnum(i) .ne. k) then k = resnum(i) nres = nres + 1 resatm(1,nres) = i if (nres .gt. 1) resatm(2,nres-1) = i - 1 end if end if end do if (nres .ge. 1) resatm(2,nres) = npdb c c close the input file and quit if no coordinates found c if (.not. opened) close (unit=ipdb) if (npdb .eq. 0) abort = .true. return end c c c ################################################################ c ## ## c ## subroutine scanpdb -- PDB chains, alternates & inserts ## c ## ## c ################################################################ c c c "scanpdb" reads the first model in a legacy PDB file and c finds chains, alternate sites, insertions and models c c subroutine scanpdb (ipdb) use iounit use pdb use sequen implicit none integer i,k,ipdb integer next,nxtlast integer length,dummy integer nalt,nins integer model,modtemp logical exist,done character*1 chain,chnlast character*1 altloc,altlast character*1 insert,inslast character*6 remark character*20 blank,text character*20 chntemp character*20 alttyp character*20 instemp character*240 record character*240 string c c c initialize chain, alternate site and insertion lists c nchain = 0 nalt = 0 nins = 0 chnlast = '#' altlast = '#' inslast = '#' blank = ' ' chnsym = '####################' altsym = ' ' alttyp = blank instyp = blank nmodel = 0 imodel = 0 c c scan for multiple chains, alternate locations and inserts c done = .false. do while (.not. done) read (ipdb,10,err=60,end=60) record 10 format (a240) remark = record(1:6) call upcase (remark) if (remark.eq.'ATOM ' .or. remark.eq.'HETATM') then next = 7 call getnumb (record,dummy,next) string = record(next+5:next+5) read (string,20) altloc 20 format (a1) string = record(next+10:next+10) read (string,30) chain 30 format (a1) next = next + 11 nxtlast = next call getnumb (record,dummy,next) if (next .eq. nxtlast) then string = record(next:next+3) read (string,40) dummy 40 format (i4) next = next + 4 end if string = record(next:next) read (string,50) insert 50 format (a1) if (chain .ne. chnlast) then if (index(chnsym,chain) .eq. 0) then nchain = nchain + 1 chnsym(nchain:nchain) = chain chnlast = chain end if end if if (altloc .ne. altlast) then if (index(alttyp,altloc) .eq. 0) then nalt = nalt + 1 alttyp(nalt:nalt) = altloc altlast = altloc end if end if if (insert .ne. inslast) then if (index(instyp,insert) .eq. 0) then nins = nins + 1 instyp(nins:nins) = insert inslast = insert end if end if else if (remark .eq. 'MODEL ') then next = 7 string = record(next:240) read (string,*) model nmodel = max(model,nmodel) else if (remark .eq. 'END ') then done = .true. end if end do 60 continue rewind (unit=ipdb) c c find out which of the multiple chains will be used c if (nchain .gt. 1) then call nextarg (chntemp,exist) if (.not. exist) then chntemp = blank if (chnsym(1:1) .eq. ' ') then string = 'BLANK=@' length = 7 else string(1:1) = chnsym(1:1) length = 1 end if do i = 2, nchain if (chnsym(i:i) .eq. ' ') then string = string(1:length)//' BLANK=@' length = length + 8 else string = string(1:length)//' '//chnsym(i:i) length = length + 2 end if end do string = string(1:length)//' [ALL]' length = length + 6 write (iout,70) string(1:length) 70 format (/,' Enter the Chain Names to Include', & ' (',a,') : ',$) read (input,80) chntemp 80 format (a20) end if call upcase (chntemp) next = 1 call gettext (chntemp,text,next) if (text.eq.blank .or. text(1:3).eq.'ALL') then chnsym = chnsym(1:nchain) else do i = 1, nchain chain = chnsym(i:i) if (chain .eq. ' ') chain = '@' k = index(chntemp,chain) if (k .eq. 0) chnsym(i:i) = '#' end do chntemp = chnsym k = 0 do i = 1, nchain chain = chntemp(i:i) if (chain .eq. '@') chain = ' ' if (chain .ne. '#') then k = k + 1 chnsym(k:k) = chain end if end do nchain = k end if end if do i = nchain+1, 20 chnsym(i:i) = '#' end do c c find out which of alternate locations will be used c if (nalt .gt. 0) then call nextarg (altsym,exist) if (.not. exist) then string(1:3) = '['//alttyp(1:1)//']' length = 3 do i = 2, nalt string = string(1:length)//' '//alttyp(i:i) length = length + 2 end do write (iout,90) string(1:length) 90 format (/,' Enter a Set of Alternate Atom Locations', & ' from (',a,') : ',$) read (input,100) record 100 format (a240) next = 1 call gettext (record,altsym,next) end if if (altsym .eq. ' ') altsym = alttyp(1:1) call upcase (altsym) end if c c find out which of the insert records will be used c if (nins .gt. 0) then call nextarg (instemp,exist) if (.not. exist) then instemp = blank string(1:1) = instyp(1:1) length = 1 do i = 2, nins string = string(1:length)//' '//instyp(i:i) length = length + 2 end do string = string(1:length)//' [ALL] NONE' length = length + 11 write (iout,110) string(1:length) 110 format (/,' Enter the Insert Records to Include', & ' (',a,') : ',$) read (input,120) instemp 120 format (a20) end if call upcase (instemp) next = 1 call gettext (instemp,text,next) if (text.eq.blank .or. text.eq.'ALL ') then instyp = instyp(1:nins) else if (text .eq. 'NONE ') then instyp = blank else instyp = instemp end if end if c c find out which of the multiple models will be used c if (nmodel .gt. 1) then call nextarg (string,exist) read (string,*,err=130,end=130) modtemp 130 continue if (.not. exist) then modtemp = 0 write (iout,140) 140 format (/,' Enter the Structural Model to Extract', & ' [0=All] : ',$) read (input,150) modtemp 150 format (i10) end if if (modtemp .ne. 0) nmodel = 1 if (modtemp .eq. 0) modtemp = 1 imodel = modtemp end if return end c c c ################################################################## c ## ## c ## subroutine fixpdb -- standard PDB atom and residue names ## c ## ## c ################################################################## c c c "fixpdb" corrects issues with PDB entries by converting residue c and atom names to the standard forms used by Tinker c c subroutine fixpdb (resname,atmname) use resdue implicit none integer i character*3 resname character*4 atmname character*7 restype c c c convert traditional 3-letter base names to PDB names c if (resname .eq. 'ADE') resname = ' A' if (resname .eq. 'GUA') resname = ' G' if (resname .eq. 'CYT') resname = ' C' if (resname .eq. 'URA') resname = ' U' if (resname .eq. 'DAD') resname = ' DA' if (resname .eq. 'DGU') resname = ' DG' if (resname .eq. 'DCY') resname = ' DC' if (resname .eq. 'THY') resname = ' DT' c c convert shifted standard base names to PDB names c if (resname .eq. 'A ') resname = ' A' if (resname .eq. 'G ') resname = ' G' if (resname .eq. 'C ') resname = ' C' if (resname .eq. 'U ') resname = ' U' if (resname .eq. ' A ') resname = ' A' if (resname .eq. ' G ') resname = ' G' if (resname .eq. ' C ') resname = ' C' if (resname .eq. ' U ') resname = ' U' if (resname .eq. 'DA ') resname = ' DA' if (resname .eq. 'DG ') resname = ' DG' if (resname .eq. 'DC ') resname = ' DC' if (resname .eq. 'DT ') resname = ' DT' c c convert terminal 3-letter base names to PDB names c if (resname .eq. 'DA5') resname = ' DA' if (resname .eq. 'DG5') resname = ' DG' if (resname .eq. 'DC5') resname = ' DC' if (resname .eq. 'DT5') resname = ' DT' if (resname .eq. 'DA3') resname = ' DA' if (resname .eq. 'DG3') resname = ' DG' if (resname .eq. 'DC3') resname = ' DC' if (resname .eq. 'DT3') resname = ' DT' c c convert unusual names for protonated histidine residues c if (resname .eq. 'HSD') resname = 'HID' if (resname .eq. 'HSE') resname = 'HIE' if (resname .eq. 'HSP') resname = 'HIS' if (resname .eq. 'HSH') resname = 'HIS' if (resname .eq. 'HIP') resname = 'HIS' if (resname .eq. 'HIH') resname = 'HIS' c c convert unusual names for other amino acid residues c if (resname .eq. 'CYN') resname = 'CYS' if (resname .eq. 'CYM') resname = 'CYD' if (resname .eq. 'LYP') resname = 'LYS' if (resname .eq. 'LYN') resname = 'LYD' if (resname .eq. 'LSN') resname = 'LYD' c c convert unusual names for terminal capping residues c if (resname .eq. 'ACP') resname = 'ACE' if (resname .eq. 'NMA') resname = 'NME' if (resname .eq. 'CT3') resname = 'NME' if (resname .eq. 'NHE') resname = 'NH2' if (resname .eq. 'CT2') resname = 'NH2' c c convert nonstandard names for water molecules c if (resname .eq. 'H2O') resname = 'HOH' if (resname .eq. 'WAT') resname = 'HOH' if (resname .eq. 'TIP') resname = 'HOH' if (resname .eq. 'DOD') resname = 'HOH' c c convert shifted and unusual names for atoms and ions c if (resname .eq. 'HE ') resname = ' HE' if (resname .eq. 'LI ') resname = ' LI' if (resname .eq. 'LI+') resname = ' LI' if (resname .eq. 'F ') resname = ' F' if (resname .eq. 'F- ') resname = ' F' if (resname .eq. 'NE ') resname = ' NE' if (resname .eq. 'NA ') resname = ' NA' if (resname .eq. 'NA+') resname = ' NA' if (resname .eq. 'SOD') resname = ' NA' if (resname .eq. 'MG ') resname = ' MG' if (resname .eq. 'MG+') resname = ' MG' if (resname .eq. 'MAG') resname = ' MG' if (resname .eq. 'CL ') resname = ' CL' if (resname .eq. 'CL-') resname = ' CL' if (resname .eq. 'CLA') resname = ' CL' if (resname .eq. 'AR ') resname = ' AR' if (resname .eq. 'K ') resname = ' K' if (resname .eq. 'K+ ') resname = ' K' if (resname .eq. 'POT') resname = ' K' if (resname .eq. 'CA ') resname = ' CA' if (resname .eq. 'CA+') resname = ' CA' if (resname .eq. 'CAL') resname = ' CA' if (resname .eq. 'FE ') resname = ' FE' if (resname .eq. 'FE+') resname = ' FE' if (resname .eq. 'ZN ') resname = ' ZN' if (resname .eq. 'ZN+') resname = ' ZN' if (resname .eq. 'BR ') resname = ' BR' if (resname .eq. 'BR-') resname = ' BR' if (resname .eq. 'KR ') resname = ' KR' if (resname .eq. 'RB ') resname = ' RB' if (resname .eq. 'RB+') resname = ' RB' if (resname .eq. 'RUB') resname = ' RB' if (resname .eq. 'SR ') resname = ' SR' if (resname .eq. 'SR+') resname = ' SR' if (resname .eq. 'I ') resname = ' I' if (resname .eq. 'I- ') resname = ' I' if (resname .eq. 'XE ') resname = ' XE' if (resname .eq. 'CS ') resname = ' CS' if (resname .eq. 'CS+') resname = ' CS' if (resname .eq. 'CES') resname = ' CS' if (resname .eq. 'BA ') resname = ' BA' if (resname .eq. 'BA+') resname = ' BA' if (resname .eq. 'BAR') resname = ' BA' c c decide whether residue is protein or nucleic acid c restype = 'UNKNOWN' do i = 1, maxamino if (resname .eq. amino(i)) restype = 'PROTEIN' end do do i = 1, maxnuc if (resname .eq. nuclz(i)) restype = 'NUCLEIC' end do c c convert unusual names common to many protein residues c if (restype .eq. 'PROTEIN') then if (atmname .eq. ' HN ') atmname = ' H ' if (atmname .eq. ' D ') atmname = ' H ' end if c c convert unusual names in protein terminal residues c if (restype .eq. 'PROTEIN') then if (atmname .eq. '1H ') atmname = ' H1 ' if (atmname .eq. ' HN1') atmname = ' H1 ' if (atmname .eq. ' HT1') atmname = ' H1 ' if (atmname .eq. '2H ') atmname = ' H2 ' if (atmname .eq. ' HN2') atmname = ' H2 ' if (atmname .eq. ' HT2') atmname = ' H2 ' if (atmname .eq. '3H ') atmname = ' H3 ' if (atmname .eq. ' HN3') atmname = ' H3 ' if (atmname .eq. ' HT3') atmname = ' H3 ' if (atmname .eq. ' O1 ') atmname = ' O ' if (atmname .eq. ' OT1') atmname = ' O ' if (atmname .eq. 'OCT1') atmname = ' O ' if (atmname .eq. ' O2 ') atmname = ' OXT' if (atmname .eq. ' OT2') atmname = ' OXT' if (atmname .eq. 'OCT2') atmname = ' OXT' if (atmname .eq. ' OT ') atmname = ' OXT' end if c c convert unusual names common to many nucleotides c if (restype .eq. 'NUCLEIC') then if (atmname .eq. ' O1P') atmname = ' OP1' if (atmname .eq. ' O2P') atmname = ' OP2' if (atmname .eq. ' O3P') atmname = ' OP3' if (atmname .eq. '2HOP') atmname = 'HOP2' if (atmname .eq. '3HOP') atmname = 'HOP3' if (atmname .eq. ' C1*') atmname = ' C1''' if (atmname .eq. ' C2*') atmname = ' C2''' if (atmname .eq. ' C3*') atmname = ' C3''' if (atmname .eq. ' C4*') atmname = ' C4''' if (atmname .eq. ' C5*') atmname = ' C5''' if (atmname .eq. ' O2*') atmname = ' O2''' if (atmname .eq. ' O3*') atmname = ' O3''' if (atmname .eq. ' O4*') atmname = ' O4''' if (atmname .eq. ' O5*') atmname = ' O5''' if (atmname .eq. ' H1*') atmname = ' H1''' if (atmname .eq. ' H2*') atmname = ' H2''' if (atmname .eq. '1H2*') atmname = ' H2''' if (atmname .eq. '2H2*') atmname = 'H2''''' if (atmname .eq. ' H3*') atmname = ' H3''' if (atmname .eq. ' H4*') atmname = ' H4''' if (atmname .eq. '1H5*') atmname = ' H5''' if (atmname .eq. '2H5*') atmname = 'H5''''' if (atmname .eq. '2HO*') atmname = 'HO2''' end if c c convert unusual names in terminal nucleotides c if (restype .eq. 'NUCLEIC') then if (atmname .eq. ' H5T') atmname = 'HO5''' if (atmname .eq. ' H3T') atmname = 'HO3''' end if c c glycine residue (GLY) c if (resname .eq. 'GLY') then if (atmname .eq. '1HA ') atmname = ' HA2' if (atmname .eq. ' HA1') atmname = ' HA3' if (atmname .eq. '2HA ') atmname = ' HA3' c c alanine residue (ALA) c else if (resname .eq. 'ALA') then if (atmname .eq. '1HB ') atmname = ' HB1' if (atmname .eq. '2HB ') atmname = ' HB2' if (atmname .eq. '3HB ') atmname = ' HB3' c c valine residue (VAL) c else if (resname .eq. 'VAL') then if (atmname .eq. '1HG1') atmname = 'HG11' if (atmname .eq. '2HG1') atmname = 'HG12' if (atmname .eq. '3HG1') atmname = 'HG13' if (atmname .eq. '1HG2') atmname = 'HG21' if (atmname .eq. '2HG2') atmname = 'HG22' if (atmname .eq. '3HG2') atmname = 'HG23' c c leucine residue (LEU) c else if (resname .eq. 'LEU') then if (atmname .eq. '1HB ') atmname = ' HB2' if (atmname .eq. ' HB1') atmname = ' HB3' if (atmname .eq. '2HB ') atmname = ' HB3' if (atmname .eq. '1HD1') atmname = 'HD11' if (atmname .eq. '2HD1') atmname = 'HD12' if (atmname .eq. '3HD1') atmname = 'HD13' if (atmname .eq. '1HD2') atmname = 'HD21' if (atmname .eq. '2HD2') atmname = 'HD22' if (atmname .eq. '3HD2') atmname = 'HD23' c c isoleucine residue (ILE) c else if (resname .eq. 'ILE') then if (atmname .eq. ' CD ') atmname = ' CD1' if (atmname .eq. '1HG1') atmname = 'HG12' if (atmname .eq. 'HG11') atmname = 'HG13' if (atmname .eq. '2HG1') atmname = 'HG13' if (atmname .eq. '1HG2') atmname = 'HG21' if (atmname .eq. '2HG2') atmname = 'HG22' if (atmname .eq. '3HG2') atmname = 'HG23' if (atmname .eq. '1HD1') atmname = 'HD11' if (atmname .eq. ' HD1') atmname = 'HD11' if (atmname .eq. '2HD1') atmname = 'HD12' if (atmname .eq. ' HD2') atmname = 'HD12' if (atmname .eq. '3HD1') atmname = 'HD13' if (atmname .eq. ' HD3') atmname = 'HD13' c c serine residue (SER) c else if (resname .eq. 'SER') then if (atmname .eq. ' OG1') atmname = ' OG ' if (atmname .eq. '1HB ') atmname = ' HB2' if (atmname .eq. ' HB1') atmname = ' HB3' if (atmname .eq. '2HB ') atmname = ' HB3' if (atmname .eq. ' HG1') atmname = ' HG ' if (atmname .eq. ' HOG') atmname = ' HG ' c c threonine residue (THR) c else if (resname .eq. 'THR') then if (atmname .eq. ' OG ') atmname = ' OG1' if (atmname .eq. ' CG ') atmname = ' CG2' if (atmname .eq. ' HOG') atmname = ' HG1' if (atmname .eq. 'HOG1') atmname = ' HG1' if (atmname .eq. '1HG2') atmname = 'HG21' if (atmname .eq. '2HG2') atmname = 'HG22' if (atmname .eq. '3HG2') atmname = 'HG23' c c cysteine residue (CYS) c else if (resname .eq. 'CYS') then if (atmname .eq. ' SG1') atmname = ' SG ' if (atmname .eq. '1HB ') atmname = ' HB2' if (atmname .eq. ' HB1') atmname = ' HB3' if (atmname .eq. '2HB ') atmname = ' HB3' if (atmname .eq. ' HG1') atmname = ' HG ' if (atmname .eq. ' HSG') atmname = ' HG ' c c proline residue (PRO) c else if (resname .eq. 'PRO') then if (atmname .eq. '1HB ') atmname = ' HB2' if (atmname .eq. ' HB1') atmname = ' HB3' if (atmname .eq. '2HB ') atmname = ' HB3' if (atmname .eq. '1HG ') atmname = ' HG2' if (atmname .eq. ' HG1') atmname = ' HG3' if (atmname .eq. '2HG ') atmname = ' HG3' if (atmname .eq. '1HD ') atmname = ' HD2' if (atmname .eq. ' HD1') atmname = ' HD3' if (atmname .eq. '2HD ') atmname = ' HD3' if (atmname .eq. ' HT1') atmname = ' H2 ' if (atmname .eq. ' HT2') atmname = ' H3 ' c c phenylalanine residue (PHE) c else if (resname .eq. 'PHE') then if (atmname .eq. '1HB ') atmname = ' HB2' if (atmname .eq. ' HB1') atmname = ' HB3' if (atmname .eq. '2HB ') atmname = ' HB3' c c tyrosine residue (TYR) c else if (resname .eq. 'TYR') then if (atmname .eq. ' HOH') atmname = ' HH ' if (atmname .eq. '1HB ') atmname = ' HB2' if (atmname .eq. ' HB1') atmname = ' HB3' if (atmname .eq. '2HB ') atmname = ' HB3' c c tryptophan residue (TRP) c else if (resname .eq. 'TRP') then if (atmname .eq. '1HB ') atmname = ' HB2' if (atmname .eq. ' HB1') atmname = ' HB3' if (atmname .eq. '2HB ') atmname = ' HB3' if (atmname .eq. ' HNE') atmname = ' HE1' c c histidine (HD and HE) residue (HIS) c else if (resname .eq. 'HIS') then if (atmname .eq. '1HB ') atmname = ' HB2' if (atmname .eq. ' HB1') atmname = ' HB3' if (atmname .eq. '2HB ') atmname = ' HB3' if (atmname .eq. ' HD ') atmname = ' HD2' if (atmname .eq. ' HE ') atmname = ' HE1' if (atmname .eq. ' HND') atmname = ' HD1' if (atmname .eq. 'HND1') atmname = ' HD1' if (atmname .eq. ' HNE') atmname = ' HE2' if (atmname .eq. 'HNE2') atmname = ' HE2' c c histidine (HD only) residue (HID) c else if (resname .eq. 'HID') then if (atmname .eq. '1HB ') atmname = ' HB2' if (atmname .eq. ' HB1') atmname = ' HB3' if (atmname .eq. '2HB ') atmname = ' HB3' if (atmname .eq. ' HD ') atmname = ' HD2' if (atmname .eq. ' HE ') atmname = ' HE1' if (atmname .eq. ' HND') atmname = ' HD1' if (atmname .eq. 'HND1') atmname = ' HD1' c c histidine (HE only) residue (HIE) c else if (resname .eq. 'HIE') then if (atmname .eq. '1HB ') atmname = ' HB2' if (atmname .eq. ' HB1') atmname = ' HB3' if (atmname .eq. '2HB ') atmname = ' HB3' if (atmname .eq. ' HD ') atmname = ' HD2' if (atmname .eq. ' HE ') atmname = ' HE1' if (atmname .eq. ' HNE') atmname = ' HE2' if (atmname .eq. 'HNE2') atmname = ' HE2' c c aspartate residue (ASP) c else if (resname .eq. 'ASP') then if (atmname .eq. '1HB ') atmname = ' HB2' if (atmname .eq. ' HB1') atmname = ' HB3' if (atmname .eq. '2HB ') atmname = ' HB3' c c asparagine residue (ASN) c else if (resname .eq. 'ASN') then if (atmname .eq. ' OD ') atmname = ' OD1' if (atmname .eq. ' ND ') atmname = ' ND2' if (atmname .eq. '1HB ') atmname = ' HB2' if (atmname .eq. ' HB1') atmname = ' HB3' if (atmname .eq. '2HB ') atmname = ' HB3' if (atmname .eq. '1HD2') atmname = 'HD21' if (atmname .eq. 'HND1') atmname = 'HD21' if (atmname .eq. '2HD2') atmname = 'HD22' if (atmname .eq. 'HND2') atmname = 'HD22' c c glutamate residue (GLU) c else if (resname .eq. 'GLU') then if (atmname .eq. '1HB ') atmname = ' HB2' if (atmname .eq. ' HB1') atmname = ' HB3' if (atmname .eq. '2HB ') atmname = ' HB3' if (atmname .eq. '1HG ') atmname = ' HG2' if (atmname .eq. ' HG1') atmname = ' HG3' if (atmname .eq. '2HG ') atmname = ' HG3' c c glutamine residue (GLN) c else if (resname .eq. 'GLN') then if (atmname .eq. ' OE ') atmname = ' OE1' if (atmname .eq. ' NE ') atmname = ' NE2' if (atmname .eq. '1HB ') atmname = ' HB2' if (atmname .eq. ' HB1') atmname = ' HB3' if (atmname .eq. '2HB ') atmname = ' HB3' if (atmname .eq. '1HG ') atmname = ' HG2' if (atmname .eq. ' HG1') atmname = ' HG3' if (atmname .eq. '2HG ') atmname = ' HG3' if (atmname .eq. '1HE2') atmname = 'HE21' if (atmname .eq. 'HNE1') atmname = 'HE21' if (atmname .eq. '2HE2') atmname = 'HE22' if (atmname .eq. 'HNE2') atmname = 'HE22' c c methionine residue (MET) c else if (resname .eq. 'MET') then if (atmname .eq. '1HB ') atmname = ' HB2' if (atmname .eq. ' HB1') atmname = ' HB3' if (atmname .eq. '2HB ') atmname = ' HB3' if (atmname .eq. '1HG ') atmname = ' HG2' if (atmname .eq. ' HG1') atmname = ' HG3' if (atmname .eq. '2HG ') atmname = ' HG3' if (atmname .eq. '1HE ') atmname = ' HE1' if (atmname .eq. '2HE ') atmname = ' HE2' if (atmname .eq. '3HE ') atmname = ' HE3' c c lysine residue (LYS) c else if (resname .eq. 'LYS') then if (atmname .eq. '1HB ') atmname = ' HB2' if (atmname .eq. ' HB1') atmname = ' HB3' if (atmname .eq. '2HB ') atmname = ' HB3' if (atmname .eq. '1HG ') atmname = ' HG2' if (atmname .eq. ' HG1') atmname = ' HG3' if (atmname .eq. '2HG ') atmname = ' HG3' if (atmname .eq. '1HD ') atmname = ' HD2' if (atmname .eq. ' HD1') atmname = ' HD3' if (atmname .eq. '2HD ') atmname = ' HD3' if (atmname .eq. '1HE ') atmname = ' HE2' if (atmname .eq. ' HE1') atmname = ' HE3' if (atmname .eq. '2HE ') atmname = ' HE3' if (atmname .eq. '1HZ ') atmname = ' HZ1' if (atmname .eq. 'HNZ1') atmname = ' HZ1' if (atmname .eq. '2HZ ') atmname = ' HZ2' if (atmname .eq. 'HNZ2') atmname = ' HZ2' if (atmname .eq. '3HZ ') atmname = ' HZ3' if (atmname .eq. 'HNZ3') atmname = ' HZ3' c c arginine residue (ARG) c else if (resname .eq. 'ARG') then if (atmname .eq. '1HB ') atmname = ' HB2' if (atmname .eq. ' HB1') atmname = ' HB3' if (atmname .eq. '2HB ') atmname = ' HB3' if (atmname .eq. '1HG ') atmname = ' HG2' if (atmname .eq. ' HG1') atmname = ' HG3' if (atmname .eq. '2HG ') atmname = ' HG3' if (atmname .eq. '1HD ') atmname = ' HD2' if (atmname .eq. ' HD1') atmname = ' HD3' if (atmname .eq. '2HD ') atmname = ' HD3' if (atmname .eq. '1HH1') atmname = 'HH11' if (atmname .eq. 'HN11') atmname = 'HH11' if (atmname .eq. '2HH1') atmname = 'HH12' if (atmname .eq. 'HN12') atmname = 'HH12' if (atmname .eq. '1HH2') atmname = 'HH21' if (atmname .eq. 'HN21') atmname = 'HH21' if (atmname .eq. '2HH2') atmname = 'HH22' if (atmname .eq. 'HN22') atmname = 'HH22' c c ornithine residue (ORN) c else if (resname .eq. 'ORN') then if (atmname .eq. '1HB ') atmname = ' HB2' if (atmname .eq. ' HB1') atmname = ' HB3' if (atmname .eq. '2HB ') atmname = ' HB3' if (atmname .eq. '1HG ') atmname = ' HG2' if (atmname .eq. ' HG1') atmname = ' HG3' if (atmname .eq. '2HG ') atmname = ' HG3' if (atmname .eq. '1HD ') atmname = ' HD2' if (atmname .eq. ' HD1') atmname = ' HD3' if (atmname .eq. '2HD ') atmname = ' HD3' if (atmname .eq. '1HE ') atmname = ' HE1' if (atmname .eq. 'HNE1') atmname = ' HE1' if (atmname .eq. '2HE ') atmname = ' HE2' if (atmname .eq. 'HNE2') atmname = ' HE2' if (atmname .eq. '3HE ') atmname = ' HE3' if (atmname .eq. 'HNE3') atmname = ' HE3' c c methylalanine residue (AIB) c else if (resname .eq. 'AIB') then if (atmname .eq. '1HB1') atmname = 'HB11' if (atmname .eq. '2HB1') atmname = 'HB12' if (atmname .eq. '3HB1') atmname = 'HB13' if (atmname .eq. '1HB2') atmname = 'HB21' if (atmname .eq. '2HB2') atmname = 'HB22' if (atmname .eq. '3HB2') atmname = 'HB23' c c pyroglutamic acid residue (PCA) c else if (resname .eq. 'PCA') then if (atmname .eq. '1HB ') atmname = ' HB2' if (atmname .eq. ' HB1') atmname = ' HB3' if (atmname .eq. '2HB ') atmname = ' HB3' if (atmname .eq. '1HG ') atmname = ' HG2' if (atmname .eq. ' HG1') atmname = ' HG3' if (atmname .eq. '2HG ') atmname = ' HG3' c c N-terminal acetyl residue (ACE) c else if (resname .eq. 'ACE') then if (atmname .eq. ' CY ') atmname = ' C ' if (atmname .eq. ' CAY') atmname = ' CH3' if (atmname .eq. ' CA ') atmname = ' CH3' if (atmname .eq. ' OY ') atmname = ' O ' if (atmname .eq. '1H ') atmname = ' H1 ' if (atmname .eq. ' HY1') atmname = ' H1 ' if (atmname .eq. '1HH3') atmname = ' H1 ' if (atmname .eq. 'HH31') atmname = ' H1 ' if (atmname .eq. '2H ') atmname = ' H2 ' if (atmname .eq. ' HY2') atmname = ' H2 ' if (atmname .eq. '2HH3') atmname = ' H2 ' if (atmname .eq. 'HH32') atmname = ' H2 ' if (atmname .eq. '3H ') atmname = ' H3 ' if (atmname .eq. ' HY3') atmname = ' H3 ' if (atmname .eq. '3HH3') atmname = ' H3 ' if (atmname .eq. 'HH33') atmname = ' H3 ' c c N-terminal formyl residue (FOR) c else if (resname .eq. 'FOR') then if (atmname .eq. ' CY ') atmname = ' C ' if (atmname .eq. ' OY ') atmname = ' O ' if (atmname .eq. ' HY ') atmname = ' H ' c c C-terminal N-methylamide residue (NME) c else if (resname .eq. 'NME') then if (atmname .eq. ' NT ') atmname = ' N ' if (atmname .eq. ' CT ') atmname = ' C ' if (atmname .eq. ' CAT') atmname = ' C ' if (atmname .eq. ' CA ') atmname = ' C ' if (atmname .eq. ' CH3') atmname = ' C ' if (atmname .eq. ' HNT') atmname = ' H ' if (atmname .eq. '1H ') atmname = ' H1 ' if (atmname .eq. '1HA ') atmname = ' H1 ' if (atmname .eq. ' HT1') atmname = ' H1 ' if (atmname .eq. '1HH3') atmname = ' H1 ' if (atmname .eq. 'HH31') atmname = ' H1 ' if (atmname .eq. '2H ') atmname = ' H2 ' if (atmname .eq. '2HA ') atmname = ' H2 ' if (atmname .eq. ' HT2') atmname = ' H2 ' if (atmname .eq. '2HH3') atmname = ' H2 ' if (atmname .eq. 'HH32') atmname = ' H2 ' if (atmname .eq. '3H ') atmname = ' H3 ' if (atmname .eq. '3HA ') atmname = ' H3 ' if (atmname .eq. ' HT3') atmname = ' H3 ' if (atmname .eq. '3HH3') atmname = ' H3 ' if (atmname .eq. 'HH33') atmname = ' H3 ' c c C-terminal amide residue (NH2) c else if (resname .eq. 'NH2') then if (atmname .eq. ' NT ') atmname = ' N ' if (atmname .eq. '1H ') atmname = ' H1 ' if (atmname .eq. '2H ') atmname = ' H2 ' if (atmname .eq. ' HT1') atmname = ' H1 ' if (atmname .eq. ' HT2') atmname = ' H2 ' c c adenosine residue (A) c else if (resname .eq. ' A') then if (atmname .eq. '1H6 ') atmname = ' H61' if (atmname .eq. '2H6 ') atmname = ' H62' c c guanosine residue (G) c else if (resname .eq. ' G') then if (atmname .eq. '1H2 ') atmname = ' H21' if (atmname .eq. '2H2 ') atmname = ' H22' c c cytidine residue (C) c else if (resname .eq. ' C') then if (atmname .eq. '1H4 ') atmname = ' H41' if (atmname .eq. '2H4 ') atmname = ' H42' c c deoxyadenosine residue (DA) c else if (resname .eq. ' DA') then if (atmname .eq. '1H6 ') atmname = ' H61' if (atmname .eq. '2H6 ') atmname = ' H62' c c deoxyguanosine residue (DG) c else if (resname .eq. ' DG') then if (atmname .eq. '1H2 ') atmname = ' H21' if (atmname .eq. '2H2 ') atmname = ' H22' c c deoxycytidine residue (DC) c else if (resname .eq. ' DC') then if (atmname .eq. '1H4 ') atmname = ' H41' if (atmname .eq. '2H4 ') atmname = ' H42' c c deoxythymidine residue (DT) c else if (resname .eq. ' DT') then if (atmname .eq. ' C5M') atmname = ' C7 ' if (atmname .eq. '1H5M') atmname = ' H71' if (atmname .eq. '2H5M') atmname = ' H72' if (atmname .eq. '3H5M') atmname = ' H73' c c water molecules (HOH) c else if (resname .eq. 'HOH') then if (atmname .eq. ' OT ') atmname = ' O ' if (atmname .eq. ' OW ') atmname = ' O ' if (atmname .eq. ' OH2') atmname = ' O ' if (atmname .eq. ' OD2') atmname = ' O ' if (atmname .eq. ' HT ') atmname = ' H ' if (atmname .eq. ' HW ') atmname = ' H ' if (atmname .eq. ' HW1') atmname = ' H ' if (atmname .eq. ' HW2') atmname = ' H ' if (atmname .eq. ' H1 ') atmname = ' H ' if (atmname .eq. ' H2 ') atmname = ' H ' if (atmname .eq. ' DT ') atmname = ' H ' if (atmname .eq. ' DW ') atmname = ' H ' if (atmname .eq. ' DW1') atmname = ' H ' if (atmname .eq. ' DW2') atmname = ' H ' if (atmname .eq. ' D1 ') atmname = ' H ' if (atmname .eq. ' D2 ') atmname = ' H ' if (atmname .eq. ' M ') atmname = ' EP ' end if return end