c c c ################################################### c ## COPYRIGHT (C) 1990 by Jay William Ponder ## c ## All Rights Reserved ## c ################################################### c c ############################################################## c ## ## c ## program protein -- build a polypeptide from sequence ## c ## ## c ############################################################## c c c "protein" builds the internal and Cartesian coordinates c of a polypeptide from amino acid sequence and torsional c angle values for the peptide backbone and side chains c c program protein use atoms use files use iounit use sequen use titles implicit none integer i,izmt integer ixyz,iseq integer natom,mode integer freeunit,trimtext logical exist,clash character*240 seqfile character*240 intfile character*240 xyzfile c c c get the name to use for the output structure files c call initial call nextarg (filename,exist) if (.not. exist) then write (iout,10) 10 format (/,' Enter Name to be Used for Output Files : ',$) read (input,20) filename 20 format (a240) end if call basefile (filename) c c get the title line for the output files c write (iout,30) 30 format (/,' Enter Title : ',$) read (input,40) title 40 format (a240) ltitle = trimtext (title) c c read the keyfile and force field parameter file c call getkey call field c c get the sequence and build Z-matrix for the structure c call getseq call prochain c c find connectivities and generate Cartesian coordinates c call connect call attach call molecule call makexyz c c perform a packing calculation for multiple chains c if (nchain .gt. 1) then call pauling call inertia (2) end if c c remove dummy atoms and set undefined atoms to type zero c natom = n do i = natom, 1, -1 if (type(i) .eq. 0) call delete (i) if (type(i) .lt. 0) type(i) = 0 end do c c convert to internal and Cartesian coordinates c mode = 0 call makeint (mode) call makexyz c c check for atom pairs with identical coordinates c clash = .false. call chkxyz (clash) c c write out a amino acid sequence file c iseq = freeunit () seqfile = filename(1:leng)//'.seq' call version (seqfile,'new') open (unit=iseq,file=seqfile,status='new') call prtseq (iseq) close (unit=iseq) c c write out an internal coordinates file c izmt = freeunit () intfile = filename(1:leng)//'.int' call version (intfile,'new') open (unit=izmt,file=intfile,status='new') call prtint (izmt) close (unit=izmt) c c write out a Cartesian coordinates file c ixyz = freeunit () xyzfile = filename(1:leng)//'.xyz' call version (xyzfile,'new') open (unit=ixyz,file=xyzfile,status='new') call prtxyz (ixyz) close (unit=ixyz) c c perform any final tasks before program exit c call final end c c c ############################################################# c ## ## c ## subroutine getseq -- amino acid sequence and angles ## c ## ## c ############################################################# c c c "getseq" asks the user for the amino acid sequence c and torsional angle values needed to define a peptide c c subroutine getseq use iounit use phipsi use resdue use sequen implicit none integer i,j,next integer length,trimtext logical done character*1 chir character*1 ucase(26) character*3 name character*240 record character*240 string data ucase / 'A','B','C','D','E','F','G','H','I','J','K','L', & 'M','N','O','P','Q','R','S','T','U','V','W','X', & 'Y','Z' / c c c provide a header to explain the method of sequence input c write (iout,10) 10 format (/,' Enter One Residue Name per Line as the Standard', & ' Three-Letter Code, and', & /,' optionally, Phi-Psi-Omega Angles (3F), Chi Angles' & ' (4F), Disulfide Partner', & /,' if CYX Residue (I), and D/L Chirality (A1)', & //,' If Only Residue Names are Entered, the Default', & ' is to Build an Extended', & /,' Conformation Using L-Amino Acids and Zwitterionic', & ' Termini', & //,' Standard Amino Acids: GLY, ALA, VAL, LEU, ILE,', & ' SER, THR, CYS, CYX, PRO,', & /,' PHE, TYR, TRP, HIS, ASP, ASN, GLU, GLN, MET, LYS,', & ' ARG, ORN, AIB', & //,' Alternative Protonation States: CYD, TYD, HID,', & ' HIE, HIP, ASH, GLH, LYD', & //,' N-Terminal Cap Residues: H2N=Deprotonated,', & ' FOR=Formyl, ACE=Acetyl,', & /,27x,'PCA=Pyroglutamic Acid', & /,' C-Terminal Cap Residues: COH=Protonated, NH2=Amide,', & ' NME=N-MethylAmide', & //,' Use Residue Name=MOL to Start a New Chain, and', & ' Use to End Input') c c initially, assume that only a single strand is present c nchain = 1 ichain(1,1) = 1 chnnam(1) = ' ' c c get the amino acid sequence data and dihedral angle values c i = 0 done = .false. do while (.not. done) i = i + 1 phi(i) = 0.0d0 psi(i) = 0.0d0 omg(i) = 0.0d0 do j = 1, 4 chi(j,i) = 0.0d0 end do chiral(i) = 1 disulf(i) = 0 chir = ' ' write (iout,20) i 20 format (/,' Enter Residue',i4,' : ',$) read (input,30) record 30 format (a240) call upcase (record) next = 1 call gettext (record,name,next) length = trimtext (name) string = record(next:240) read (string,*,err=40,end=40) phi(i),psi(i),omg(i), & (chi(j,i),j=1,4),disulf(i) 40 continue call getword (record,chir,next) c c handle special names used for certain amino acids c if (name .eq. 'CYH') name = 'CYS' if (name .eq. 'CSS') name = 'CYX' if (name .eq. 'HIP') name = 'HIS' c c disulfide bridged residues are cystine instead of cysteine c if (name(1:1).eq.'C' .and. disulf(i).ne.0) then length = 3 name = 'CYX' end if c c check the D/L chirality of the current residue c if (chir .eq. 'D') chiral(i) = -1 c c process and store the current amino acid residue type c if (name .eq. 'MOL') then i = i - 1 ichain(2,nchain) = i nchain = nchain + 1 ichain(1,nchain) = i + 1 else if (name .eq. ' ') then done = .true. nseq = i - 1 ichain(2,nchain) = nseq else seq(i) = amino(maxamino) seqtyp(i) = 0 if (length .eq. 1) then do j = 1, maxamino if (name(1:1) .eq. amino1(j)) then seq(i) = amino(j) seqtyp(i) = j end if end do else if (length .eq. 3) then do j = 1, maxamino if (name .eq. amino(j)) then seq(i) = amino(j) seqtyp(i) = j end if end do end if if (seqtyp(i) .eq. 0) then i = i - 1 write (iout,50) name 50 format (/,' GETSEQ -- Amino Acid Type ',a3, & ' is Not Supported') end if end if end if end do c c set chain identifiers if multiple chains are present c if (nchain .gt. 1) then do i = 1, nchain chnnam(i) = ucase(i) end do end if c c set default values for the phi-psi-omega-chi angles; c use extended values if no phi-psi values were given c do i = 1, nseq if (phi(i).eq.0.0d0 .and. psi(i).eq.0.0d0) then phi(i) = -135.0d0 if (seq(i) .eq. 'PRO') phi(i) = -60.0d0 psi(i) = 135.0d0 end if if (omg(i) .eq. 0.0d0) then omg(i) = 180.0d0 end if if (chi(1,i) .eq. 0.0d0) then do j = 1, 4 chi(j,i) = 180.0d0 if (seq(i) .eq. 'PRO') chi(j,i) = 0.0d0 if (seq(i) .eq. 'PCA') chi(j,i) = 0.0d0 end do if (seq(i) .eq. 'LEU') chi(2,i) = 60.0d0 if (seq(i) .eq. 'PHE') chi(2,i) = 90.0d0 if (seq(i) .eq. 'TYR') chi(2,i) = 90.0d0 if (seq(i) .eq. 'TYD') chi(2,i) = 90.0d0 if (seq(i) .eq. 'TRP') chi(2,i) = 90.0d0 if (seq(i) .eq. 'HIS') chi(2,i) = 90.0d0 if (seq(i) .eq. 'HID') chi(2,i) = 90.0d0 if (seq(i) .eq. 'HIE') chi(2,i) = 90.0d0 end if c c check for the presence of any disulfide bonds c if (disulf(i) .ne. 0) then if (seq(i) .ne. 'CYX') then write (iout,60) i 60 format (' GETSEQ -- Error in Disulfide Bond', & ' at Residue',i5) end if if (i.lt.disulf(i) .and. disulf(disulf(i)).ne.i) then write (iout,70) i,disulf(i) 70 format (' GETSEQ -- Error in Disulfide Bond', & ' at Residue',i5,' or',i5) end if end if end do return end c c c ########################################################### c ## ## c ## subroutine prochain -- build polypeptide backbone ## c ## ## c ########################################################### c c c "prochain" builds up the internal coordinates for an amino c acid sequence from the phi, psi, omega and chi values c c subroutine prochain use atoms use iounit use phipsi use resdue use sequen implicit none integer i,k,m integer next,nsave integer, allocatable :: ni(:) integer, allocatable :: cai(:) integer, allocatable :: ci(:) logical single,cyclic character*1 answer character*3 resname character*240 record c c c determine whether the peptide chain is cyclic c cyclic = .false. write (iout,10) 10 format (/,' Cyclize the Polypeptide Chain [N] : ',$) read (input,20) record 20 format (a240) next = 1 call gettext (record,answer,next) call upcase (answer) if (answer .eq. 'Y') cyclic = .true. c c perform dynamic allocation of some local arrays c allocate (ni(nseq)) allocate (cai(nseq)) allocate (ci(nseq)) c c initialize the atom counter to the first atom c n = 1 c c set the first residue number and get the type and name c do m = 1, nchain single = .false. if (ichain(1,m) .eq. ichain(2,m)) single = .true. i = ichain(1,m) k = seqtyp(i) resname = amino(k) c c build the first residue for a cyclic peptide c if (cyclic) then if (m .eq. 1) then ni(i) = n call zatom (ntyp(k),0.0d0,0.0d0,0.0d0,0,0,0,0) cai(i) = n call zatom (catyp(k),1.46d0,0.0d0,0.0d0,ni(i),0,0,0) ci(i) = n call zatom (ctyp(k),1.51d0,110.7d0,0.0d0, & cai(i),ni(i),0,0) else ni(i) = n call zatom (ntyp(k),30.0d0,150.0d0,180.0d0,n-1,n-2,n-3,0) call zatom (-2,0.0d0,0.0d0,0.0d0,n-2,n-1,0,0) cai(i) = n call zatom (catyp(k),1.46d0,150.0d0,180.0d0, & ni(i),n-2,n-3,0) ci(i) = n call zatom (ctyp(k),1.51d0,110.7d0,180.0d0, & cai(i),ni(i),n-3,0) end if call zatom (otyp(k),1.22d0,122.5d0,psi(i)-180.0d0, & ci(i),cai(i),ni(i),0) call zatom (hntyp(k),1.02d0,121.0d0,phi(i)-180.0d0, & ni(i),cai(i),ci(i),0) call zatom (hatyp(k),1.11d0,109.5d0,107.9d0, & cai(i),ni(i),ci(i),-chiral(i)) call proside (resname,i,cai(i),ni(i),ci(i)) c c build the first residue as an N-terminal formyl group c else if (resname .eq. 'FOR') then if (m .eq. 1) then ci(i) = n call zatom (cntyp(k),0.0d0,0.0d0,0.0d0,0,0,0,0) ni(i) = n call zatom (ontyp(k),1.22d0,0.0d0,0.0d0,n-1,0,0,0) cai(i) = n call zatom (hantyp(k),1.12d0,120.0d0,0.0d0,n-2,n-1,0,0) else ci(i) = n call zatom (cntyp(k),30.0d0,150.0d0,180.0d0, & n-1,n-2,n-3,0) call zatom (-2,0.0d0,0.0d0,0.0d0,n-2,n-1,0,0) ni(i) = n call zatom (ontyp(k),1.22d0,150.0d0,180.0d0, & n-1,n-2,n-3,0) cai(i) = n call zatom (hantyp(k),1.12d0,120.0d0,0.0d0,n-2,n-1,n-3,0) end if psi(i) = 180.0d0 c c build the first residue as an N-terminal acetyl group c else if (resname .eq. 'ACE') then if (m .eq. 1) then cai(i) = n call zatom (cantyp(k),0.0d0,0.0d0,0.0d0,0,0,0,0) ci(i) = n call zatom (cntyp(k),1.51d0,0.0d0,0.0d0,n-1,0,0,0) call zatom (ontyp(k),1.22d0,122.5d0,0.0d0,n-1,n-2,0,0) else cai(i) = n call zatom (cantyp(k),30.0d0,150.0d0,180.0d0, & n-1,n-2,n-3,0) call zatom (-2,0.0d0,0.0d0,0.0d0,n-2,n-1,0,0) ci(i) = n call zatom (cntyp(k),1.51d0,150.0d0,180.0d0, & n-1,n-2,n-3,0) call zatom (ontyp(k),1.22d0,122.5d0,0.0d0, & n-1,n-2,n-3,0) end if ni(i) = n call zatom (hantyp(k),1.11d0,107.9d0,0.0d0,n-3,n-2,n-1,0) call zatom (hantyp(k),1.11d0,107.9d0,109.4d0,n-4,n-3,n-1,1) call zatom (hantyp(k),1.11d0,107.9d0,109.4d0,n-5,n-4,n-2,-1) psi(i) = 180.0d0 c c build the first residue as a proline c else if (resname .eq. 'PRO') then if (m .eq. 1) then ni(i) = n call zatom (nntyp(k),0.0d0,0.0d0,0.0d0,0,0,0,0) cai(i) = n call zatom (cantyp(k),1.50d0,0.0d0,0.0d0,ni(i),0,0,0) ci(i) = n if (single) then call zatom (cctyp(k),1.51d0,111.6d0,0.0d0, & cai(i),ni(i),0,0) else call zatom (cntyp(k),1.51d0,110.7d0,0.0d0, & cai(i),ni(i),0,0) end if else ni(i) = n call zatom (nntyp(k),30.0d0,150.0d0,180.0d0, & n-1,n-2,n-3,0) call zatom (-2,0.0d0,0.0d0,0.0d0,n-2,n-1,0,0) cai(i) = n call zatom (cantyp(k),1.50d0,150.0d0,180.0d0, & ni(i),n-2,n-3,0) ci(i) = n if (single) then call zatom (cctyp(k),1.51d0,111.6d0,180.0d0, & cai(i),ni(i),n-3,0) else call zatom (cntyp(k),1.51d0,110.7d0,180.0d0, & cai(i),ni(i),n-3,0) end if end if if (single) then call zatom (octyp(k),1.25d0,117.0d0,psi(1)-180.0d0, & ci(i),cai(i),ni(i),0) else call zatom (ontyp(k),1.22d0,122.5d0,psi(1)-180.0d0, & ci(i),cai(i),ni(i),0) end if call zatom (hnntyp(k),1.02d0,109.5d0,0.0d0, & ni(i),cai(i),ci(i),0) call zatom (hnntyp(k),1.02d0,109.5d0,-120.0d0, & ni(i),cai(i),ci(i),0) call zatom (hantyp(k),1.11d0,109.5d0,107.9d0, & cai(i),ni(i),ci(i),-chiral(i)) call proside (resname,i,cai(i),ni(i),ci(i)) c c build the first residue as a pyroglutamic acid c else if (resname .eq. 'PCA') then if (m .eq. 1) then ni(i) = n call zatom (nntyp(k),0.0d0,0.0d0,0.0d0,0,0,0,0) cai(i) = n call zatom (cantyp(k),1.50d0,0.0d0,0.0d0,ni(i),0,0,0) ci(i) = n if (single) then call zatom (cctyp(k),1.51d0,111.6d0,0.0d0, & cai(i),ni(i),0,0) else call zatom (cntyp(k),1.51d0,110.7d0,0.0d0, & cai(i),ni(i),0,0) end if else ni(i) = n call zatom (nntyp(k),30.0d0,150.0d0,180.0d0, & n-1,n-2,n-3,0) call zatom (-2,0.0d0,0.0d0,0.0d0,n-2,n-1,0,0) cai(i) = n call zatom (cantyp(k),1.50d0,150.0d0,180.0d0, & ni(i),n-2,n-3,0) ci(i) = n if (single) then call zatom (cctyp(k),1.51d0,111.6d0,180.0d0, & cai(i),ni(i),n-3,0) else call zatom (cntyp(k),1.51d0,110.7d0,180.0d0, & cai(i),ni(i),n-3,0) end if end if if (single) then call zatom (octyp(k),1.25d0,117.0d0,psi(1)-180.0d0, & ci(i),cai(i),ni(i),0) else call zatom (ontyp(k),1.22d0,122.5d0,psi(1)-180.0d0, & ci(i),cai(i),ni(i),0) end if call zatom (hnntyp(k),1.02d0,109.5d0,-60.0d0, & ni(i),cai(i),ci(i),0) call zatom (hantyp(k),1.11d0,109.5d0,107.9d0, & cai(i),ni(i),ci(i),-chiral(i)) call proside (resname,i,cai(i),ni(i),ci(i)) c c build the first residue for N-terminal deprotonated amino acids c else if (resname .eq. 'H2N') then i = i + 1 k = seqtyp(i) resname = amino(k) if (m .eq. 1) then ni(i) = n k = seqtyp(i-1) call zatom (nntyp(k),0.0d0,0.0d0,0.0d0,0,0,0,0) k = seqtyp(i) cai(i) = n call zatom (cantyp(k),1.50d0,0.0d0,0.0d0,ni(i),0,0,0) ci(i) = n if (single) then call zatom (cctyp(k),1.51d0,111.6d0,0.0d0, & cai(i),ni(i),0,0) else call zatom (cntyp(k),1.51d0,110.7d0,0.0d0, & cai(i),ni(i),0,0) end if else ni(i) = n k = seqtyp(i-1) call zatom (nntyp(k),30.0d0,150.0d0,180.0d0, & n-1,n-2,n-3,0) k = seqtyp(i) call zatom (-2,0.0d0,0.0d0,0.0d0,n-2,n-1,0,0) cai(i) = n call zatom (cantyp(k),1.50d0,150.0d0,180.0d0, & ni(i),n-2,n-3,0) ci(i) = n if (single) then call zatom (cctyp(k),1.51d0,111.6d0,180.0d0, & cai(i),ni(i),n-3,0) else call zatom (cntyp(k),1.51d0,110.7d0,180.0d0, & cai(i),ni(i),n-3,0) end if end if if (single) then call zatom (octyp(k),1.25d0,117.0d0,psi(1)-180.0d0, & ci(i),cai(i),ni(i),0) else call zatom (ontyp(k),1.22d0,122.5d0,psi(1)-180.0d0, & ci(i),cai(i),ni(i),0) end if k = seqtyp(i-1) if (resname .eq. 'PRO') then call zatom (hnntyp(k),1.02d0,124.5d0,phi(i), & ni(i),cai(i),ci(i),0) else call zatom (hnntyp(k),1.02d0,109.5d0,phi(i), & ni(i),cai(i),ci(i),0) call zatom (hnntyp(k),1.02d0,109.5d0,108.0d0, & ni(i),cai(i),n-1,1) end if k = seqtyp(i) call zatom (hantyp(k),1.11d0,109.5d0,107.9d0, & cai(i),ni(i),ci(i),-chiral(i)) call proside (resname,i,cai(i),ni(i),ci(i)) c c build the first residue for all other standard amino acids c else if (m .eq. 1) then ni(i) = n call zatom (nntyp(k),0.0d0,0.0d0,0.0d0,0,0,0,0) cai(i) = n call zatom (cantyp(k),1.50d0,0.0d0,0.0d0,ni(i),0,0,0) ci(i) = n if (single) then call zatom (cctyp(k),1.51d0,111.6d0,0.0d0, & cai(i),ni(i),0,0) else call zatom (cntyp(k),1.51d0,110.7d0,0.0d0, & cai(i),ni(i),0,0) end if else ni(i) = n call zatom (nntyp(k),30.0d0,150.0d0,180.0d0, & n-1,n-2,n-3,0) call zatom (-2,0.0d0,0.0d0,0.0d0,n-2,n-1,0,0) cai(i) = n call zatom (cantyp(k),1.50d0,150.0d0,180.0d0, & ni(i),n-2,n-3,0) ci(i) = n if (single) then call zatom (cctyp(k),1.51d0,111.6d0,180.0d0, & cai(i),ni(i),n-3,0) else call zatom (cntyp(k),1.51d0,110.7d0,180.0d0, & cai(i),ni(i),n-3,0) end if end if if (single) then call zatom (octyp(k),1.25d0,117.0d0,psi(1)-180.0d0, & ci(i),cai(i),ni(i),0) else call zatom (ontyp(k),1.22d0,122.5d0,psi(1)-180.0d0, & ci(i),cai(i),ni(i),0) end if call zatom (hnntyp(k),1.02d0,109.5d0,phi(i), & ni(i),cai(i),ci(i),0) call zatom (hnntyp(k),1.02d0,109.5d0,108.0d0, & ni(i),cai(i),n-1,1) call zatom (hnntyp(k),1.02d0,109.5d0,108.0d0, & ni(i),cai(i),n-2,-1) call zatom (hantyp(k),1.11d0,109.5d0,107.9d0, & cai(i),ni(i),ci(i),-chiral(i)) call proside (resname,i,cai(i),ni(i),ci(i)) end if c c build atoms for residues in the middle of the chain c do while (i .lt. ichain(2,m)-1) i = i + 1 k = seqtyp(i) resname = amino(k) ni(i) = n call zatom (ntyp(k),1.34d0,112.7d0,psi(i-1), & ci(i-1),cai(i-1),ni(i-1),0) cai(i) = n call zatom (catyp(k),1.46d0,121.0d0,omg(i-1), & ni(i),ci(i-1),cai(i-1),0) ci(i) = n call zatom (ctyp(k),1.51d0,111.6d0,phi(i), & cai(i),ni(i),ci(i-1),0) call zatom (otyp(k),1.22d0,122.5d0,psi(i)-180.0d0, & ci(i),cai(i),ni(i),0) call zatom (hntyp(k),1.02d0,121.0d0,phi(i)-180.0d0, & ni(i),cai(i),ci(i),0) call zatom (hatyp(k),1.11d0,109.5d0,107.9d0, & cai(i),ni(i),ci(i),-chiral(i)) call proside (resname,i,cai(i),ni(i),ci(i)) end do c c set the number and type of the last residue c i = ichain(2,m) k = seqtyp(i) resname = amino(k) c c build the last residue for a cyclic peptide c if (cyclic) then ni(i) = n call zatom (ntyp(k),1.34d0,112.7d0,psi(i-1), & ci(i-1),cai(i-1),ni(i-1),0) cai(i) = n call zatom (catyp(k),1.46d0,121.0d0,omg(i-1), & ni(i),ci(i-1),cai(i-1),0) ci(i) = n call zatom (ctyp(k),1.51d0,111.6d0,phi(i), & cai(i),ni(i),ci(i-1),0) call zatom (-1,0.0d0,0.0d0,0.0d0,ni(1),ci(i),0,0) call zatom (otyp(k),1.22d0,122.5d0,psi(i)-180.0d0, & ci(i),cai(i),ni(i),0) call zatom (hntyp(k),1.02d0,121.0d0,phi(i)-180.0d0, & ni(i),cai(i),ci(i),0) call zatom (hatyp(k),1.11d0,109.5d0,107.9d0, & cai(i),ni(i),ci(i),-chiral(i)) call proside (resname,i,cai(i),ni(i),ci(i)) c c build the last residue as a C-terminal amide c else if (resname .eq. 'NH2') then call zatom (nctyp(k),1.34d0,112.7d0,psi(i-1), & ci(i-1),cai(i-1),ni(i-1),0) call zatom (hnctyp(k),1.02d0,119.0d0,0.0d0, & n-1,ci(i-1),cai(i-1),0) call zatom (hnctyp(k),1.02d0,119.0d0,180.0d0, & n-2,ci(i-1),cai(i-1),0) c c build the last residue as a C-terminal N-methylamide c else if (resname .eq. 'NME') then call zatom (nctyp(k),1.34d0,112.7d0,psi(i-1), & ci(i-1),cai(i-1),ni(i-1),0) call zatom (cactyp(k),1.46d0,121.0d0,180.0d0, & n-1,ci(i-1),cai(i-1),0) call zatom (hnctyp(k),1.02d0,118.0d0,121.0d0, & n-2,ci(i-1),n-1,1) call zatom (hactyp(k),1.11d0,109.5d0,180.0d0, & n-2,n-3,ci(i-1),0) call zatom (hactyp(k),1.11d0,109.5d0,109.5d0, & n-3,n-4,n-1,1) call zatom (hactyp(k),1.11d0,109.5d0,109.5d0, & n-4,n-5,n-2,-1) c c build the last residue as a protonated C-terminal amino acid c else if (resname .eq. 'COH') then nsave = n n = ci(i-1) call zatom (cctyp(k),1.51d0,111.6d0,phi(i), & cai(i-1),ni(i-1),ci(i-2),0) call zatom (octyp(k),1.22d0,122.5d0,psi(i)-180.0d0, & ci(i-1),cai(i-1),ni(i-1),0) n = nsave call zatom (nctyp(k),1.35d0,112.7d0,psi(i-1), & ci(i-1),cai(i-1),ni(i-1),0) call zatom (hnctyp(k),0.98d0,108.7d0,180.0d0, & n-1,ci(i-1),cai(i-1),0) c c build the last residue for all other standard amino acids c else if (.not. single) then ni(i) = n call zatom (nctyp(k),1.34d0,112.7d0,psi(i-1), & ci(i-1),cai(i-1),ni(i-1),0) cai(i) = n call zatom (cactyp(k),1.46d0,121.0d0,omg(i-1), & ni(i),ci(i-1),cai(i-1),0) ci(i) = n call zatom (cctyp(k),1.51d0,111.6d0,phi(i), & cai(i),ni(i),ci(i-1),0) call zatom (octyp(k),1.25d0,117.0d0,psi(i)-180.0d0, & ci(i),cai(i),ni(i),0) call zatom (hnctyp(k),1.02d0,121.0d0,phi(i)-180.0d0, & ni(i),cai(i),ci(i),0) call zatom (hactyp(k),1.11d0,109.5d0,107.9d0, & cai(i),ni(i),ci(i),-chiral(i)) call proside (resname,i,cai(i),ni(i),ci(i)) end if call zatom (octyp(k),1.25d0,117.0d0,psi(i), & ci(i),cai(i),ni(i),0) end if end do c c finally, set the total number of atoms c n = n - 1 c c perform deallocation of some local arrays c deallocate (ni) deallocate (cai) deallocate (ci) return end c c c ########################################################### c ## ## c ## subroutine proside -- build amino acid side chain ## c ## ## c ########################################################### c c c "proside" builds the side chain for a single amino acid c residue in terms of internal coordinates c c resname 3-letter name of current amino acid residue c i number of the current amino acid residue c cai atom number of alpha carbon in residue i c ni atom number of amide nitrogen in residue i c ci atom number of carbonyl carbon in residue i c c note biotypes of CD and HD atoms for N-terminal proline c are set as absolute values, not relative to the CB atom c c subroutine proside (resname,i,cai,ni,ci) use atoms use phipsi use resdue use sequen implicit none integer i,k integer cai,ni,ci integer ntprocd integer ntprohd character*3 resname c c c set the CB atom as reference site c k = cbtyp(seqtyp(i)) c c set biotypes for CD and HD of N-terminal PRO residue c ntprocd = 469 ntprohd = 470 c c glycine residue (GLY) c if (resname .eq. 'GLY') then k = hatyp(seqtyp(i)) if (i .eq. 1) k = hantyp(seqtyp(i)) if (i .eq. nseq) k = hactyp(seqtyp(i)) call zatom (k,1.11d0,109.5d0,107.9d0,cai,ni,ci,chiral(i)) c c alanine residue (ALA) c else if (resname .eq. 'ALA') then call zatom (k,1.54d0,109.5d0,107.8d0,cai,ni,ci,chiral(i)) call zatom (k+1,1.11d0,109.4d0,chi(1,i),n-1,cai,ni,0) call zatom (k+1,1.11d0,109.4d0,109.4d0,n-2,cai,n-1,1) call zatom (k+1,1.11d0,109.4d0,109.4d0,n-3,cai,n-2,-1) c c valine residue (VAL) c else if (resname .eq. 'VAL') then call zatom (k,1.54d0,109.5d0,107.8d0,cai,ni,ci,chiral(i)) call zatom (k+2,1.54d0,109.5d0,chi(1,i),n-1,cai,ni,0) call zatom (k+4,1.54d0,109.5d0,109.5d0,n-2,cai,n-1,-1) call zatom (k+1,1.11d0,109.4d0,109.4d0,n-3,cai,n-2,1) call zatom (k+3,1.11d0,109.4d0,180.0d0,n-3,n-4,cai,0) call zatom (k+3,1.11d0,109.4d0,109.4d0,n-4,n-5,n-1,1) call zatom (k+3,1.11d0,109.4d0,109.4d0,n-5,n-6,n-2,-1) call zatom (k+5,1.11d0,109.4d0,180.0d0,n-5,n-7,cai,0) call zatom (k+5,1.11d0,109.4d0,109.4d0,n-6,n-8,n-1,1) call zatom (k+5,1.11d0,109.4d0,109.4d0,n-7,n-9,n-2,-1) c c leucine residue (LEU) c else if (resname .eq. 'LEU') then call zatom (k,1.54d0,109.5d0,107.8d0,cai,ni,ci,chiral(i)) call zatom (k+2,1.54d0,109.5d0,chi(1,i),n-1,cai,ni,0) call zatom (k+4,1.54d0,109.5d0,chi(2,i),n-1,n-2,cai,0) call zatom (k+6,1.54d0,109.5d0,109.4d0,n-2,n-3,n-1,-1) call zatom (k+1,1.11d0,109.4d0,109.4d0,n-4,cai,n-3,1) call zatom (k+1,1.11d0,109.4d0,109.4d0,n-5,cai,n-4,-1) call zatom (k+3,1.11d0,109.4d0,109.4d0,n-5,n-6,n-4,1) call zatom (k+5,1.11d0,109.4d0,180.0d0,n-5,n-6,n-7,0) call zatom (k+5,1.11d0,109.4d0,109.4d0,n-6,n-7,n-1,1) call zatom (k+5,1.11d0,109.4d0,109.4d0,n-7,n-8,n-2,-1) call zatom (k+7,1.11d0,109.4d0,180.0d0,n-7,n-9,n-10,0) call zatom (k+7,1.11d0,109.4d0,109.4d0,n-8,n-10,n-1,1) call zatom (k+7,1.11d0,109.4d0,109.4d0,n-9,n-11,n-2,-1) c c isoleucine residue (ILE) c else if (resname .eq. 'ILE') then call zatom (k,1.54d0,109.5d0,109.5d0,cai,ni,ci,chiral(i)) call zatom (k+2,1.54d0,109.5d0,chi(1,i),n-1,cai,ni,0) call zatom (k+4,1.54d0,109.5d0,109.5d0,n-2,cai,n-1,1) call zatom (k+6,1.54d0,109.5d0,chi(2,i),n-2,n-3,cai,0) call zatom (k+1,1.11d0,109.4d0,109.4d0,n-4,cai,n-3,-1) call zatom (k+3,1.11d0,109.4d0,109.4d0,n-4,n-5,n-2,1) call zatom (k+3,1.11d0,109.4d0,109.4d0,n-5,n-6,n-3,-1) call zatom (k+5,1.11d0,110.0d0,180.0d0,n-5,n-7,n-6,0) call zatom (k+5,1.11d0,110.0d0,109.0d0,n-6,n-8,n-1,1) call zatom (k+5,1.11d0,110.0d0,109.0d0,n-7,n-9,n-2,-1) call zatom (k+7,1.11d0,110.0d0,180.0d0,n-7,n-9,n-10,0) call zatom (k+7,1.11d0,110.0d0,109.0d0,n-8,n-10,n-1,1) call zatom (k+7,1.11d0,110.0d0,109.0d0,n-9,n-11,n-2,-1) c c serine residue (SER) c else if (resname .eq. 'SER') then call zatom (k,1.54d0,109.5d0,107.8d0,cai,ni,ci,chiral(i)) call zatom (k+2,1.41d0,107.5d0,chi(1,i),n-1,cai,ni,0) call zatom (k+1,1.11d0,109.4d0,106.7d0,n-2,cai,n-1,1) call zatom (k+1,1.11d0,109.4d0,106.7d0,n-3,cai,n-2,-1) call zatom (k+3,0.94d0,106.9d0,chi(2,i),n-3,n-4,cai,0) c c threonine residue (THR) c else if (resname .eq. 'THR') then call zatom (k,1.54d0,109.5d0,109.5d0,cai,ni,ci,chiral(i)) call zatom (k+2,1.41d0,107.5d0,chi(1,i),n-1,cai,ni,0) call zatom (k+4,1.54d0,109.5d0,107.7d0,n-2,cai,n-1,1) call zatom (k+1,1.11d0,109.4d0,106.7d0,n-3,cai,n-2,-1) call zatom (k+3,0.94d0,106.9d0,chi(2,i),n-3,n-4,cai,0) call zatom (k+5,1.11d0,110.0d0,180.0d0,n-3,n-5,cai,0) call zatom (k+5,1.11d0,110.0d0,109.0d0,n-4,n-6,n-1,1) call zatom (k+5,1.11d0,110.0d0,109.0d0,n-5,n-7,n-2,-1) c c cysteine residue (CYS) c else if (resname .eq. 'CYS') then call zatom (k,1.54d0,109.5d0,107.8d0,cai,ni,ci,chiral(i)) call zatom (k+2,1.82d0,109.0d0,chi(1,i),n-1,cai,ni,0) call zatom (k+1,1.11d0,109.4d0,112.0d0,n-2,cai,n-1,1) call zatom (k+1,1.11d0,109.4d0,112.0d0,n-3,cai,n-2,-1) call zatom (k+3,1.34d0,96.0d0,chi(2,i),n-3,n-4,cai,0) c c cystine residue (CYX) c else if (resname .eq. 'CYX') then call zatom (k,1.54d0,109.5d0,107.8d0,cai,ni,ci,chiral(i)) call zatom (k+2,1.82d0,109.0d0,chi(1,i),n-1,cai,ni,0) call zatom (k+1,1.11d0,109.4d0,112.0d0,n-2,cai,n-1,1) call zatom (k+1,1.11d0,109.4d0,112.0d0,n-3,cai,n-2,-1) if (disulf(i) .gt. i) then disulf(i) = n - 3 else if (disulf(i) .lt. i) then call zatom (-1,0.0d0,0.0d0,0.0d0,disulf(disulf(i)),n-3,0,0) end if c c deprotonated cysteine residue (CYD) c else if (resname .eq. 'CYD') then call zatom (k,1.54d0,109.5d0,107.8d0,cai,ni,ci,chiral(i)) call zatom (k+2,1.82d0,109.0d0,chi(1,i),n-1,cai,ni,0) call zatom (k+1,1.11d0,109.4d0,112.0d0,n-2,cai,n-1,1) call zatom (k+1,1.11d0,109.4d0,112.0d0,n-3,cai,n-2,-1) c c proline residue (PRO) c else if (resname .eq. 'PRO') then call zatom (k,1.54d0,107.0d0,109.5d0,cai,ni,ci,chiral(i)) call zatom (k+2,1.54d0,107.0d0,chi(1,i),n-1,cai,ni,0) if (i .eq. 1) then call zatom (ntprocd,1.54d0,107.0d0,chi(2,i),n-1,n-2,cai,0) else call zatom (k+4,1.54d0,107.0d0,chi(2,i),n-1,n-2,cai,0) end if call zatom (-1,0.0d0,0.0d0,0.0d0,ni,n-1,0,0) call zatom (k+1,1.11d0,109.4d0,109.4d0,n-3,cai,n-2,1) call zatom (k+1,1.11d0,109.4d0,109.4d0,n-4,cai,n-3,-1) call zatom (k+3,1.11d0,109.4d0,109.4d0,n-4,n-5,n-3,1) call zatom (k+3,1.11d0,109.4d0,109.4d0,n-5,n-6,n-4,-1) if (i .eq. 1) then call zatom (ntprohd,1.11d0,109.4d0,109.4d0,n-5,n-6,ni,1) call zatom (ntprohd,1.11d0,109.4d0,109.4d0,n-6,n-7,ni,-1) else call zatom (k+5,1.11d0,109.4d0,109.4d0,n-5,n-6,ni,1) call zatom (k+5,1.11d0,109.4d0,109.4d0,n-6,n-7,ni,-1) end if c c phenylalanine residue (PHE) c else if (resname .eq. 'PHE') then call zatom (k,1.54d0,109.5d0,107.8d0,cai,ni,ci,chiral(i)) call zatom (k+2,1.50d0,109.5d0,chi(1,i),n-1,cai,ni,0) call zatom (k+3,1.39d0,120.0d0,chi(2,i),n-1,n-2,cai,0) call zatom (k+3,1.39d0,120.0d0,120.0d0,n-2,n-3,n-1,1) call zatom (k+5,1.39d0,120.0d0,180.0d0,n-2,n-3,n-4,0) call zatom (k+5,1.39d0,120.0d0,180.0d0,n-2,n-4,n-5,0) call zatom (k+7,1.39d0,120.0d0,0.0d0,n-2,n-4,n-5,0) call zatom (-1,0.0d0,0.0d0,0.0d0,n-2,n-1,0,0) call zatom (k+1,1.11d0,109.4d0,109.4d0,n-7,cai,n-6,1) call zatom (k+1,1.11d0,109.4d0,109.4d0,n-8,cai,n-7,-1) call zatom (k+4,1.10d0,120.0d0,120.0d0,n-7,n-8,n-5,1) call zatom (k+4,1.10d0,120.0d0,120.0d0,n-7,n-9,n-5,1) call zatom (k+6,1.10d0,120.0d0,120.0d0,n-7,n-9,n-5,1) call zatom (k+6,1.10d0,120.0d0,120.0d0,n-7,n-9,n-6,1) call zatom (k+8,1.10d0,120.0d0,120.0d0,n-7,n-9,n-8,1) c c tyrosine residue (TYR) c else if (resname .eq. 'TYR') then call zatom (k,1.54d0,109.5d0,107.8d0,cai,ni,ci,chiral(i)) call zatom (k+2,1.50d0,109.5d0,chi(1,i),n-1,cai,ni,0) call zatom (k+3,1.39d0,120.0d0,chi(2,i),n-1,n-2,cai,0) call zatom (k+3,1.39d0,120.0d0,120.0d0,n-2,n-3,n-1,1) call zatom (k+5,1.39d0,120.0d0,180.0d0,n-2,n-3,n-4,0) call zatom (k+5,1.39d0,120.0d0,180.0d0,n-2,n-4,n-5,0) call zatom (k+7,1.39d0,120.0d0,0.0d0,n-2,n-4,n-5,0) call zatom (-1,0.0d0,0.0d0,0.0d0,n-2,n-1,0,0) call zatom (k+8,1.36d0,120.0d0,120.0d0,n-1,n-2,n-3,1) call zatom (k+1,1.11d0,109.4d0,109.4d0,n-8,cai,n-7,1) call zatom (k+1,1.11d0,109.4d0,109.4d0,n-9,cai,n-8,-1) call zatom (k+4,1.10d0,120.0d0,120.0d0,n-8,n-9,n-6,1) call zatom (k+4,1.10d0,120.0d0,120.0d0,n-8,n-10,n-6,1) call zatom (k+6,1.10d0,120.0d0,120.0d0,n-8,n-10,n-6,1) call zatom (k+6,1.10d0,120.0d0,120.0d0,n-8,n-10,n-7,1) call zatom (k+9,0.97d0,108.0d0,0.0d0,n-7,n-8,n-9,0) c c deprotonated tyrosine residue (TYD) c else if (resname .eq. 'TYD') then call zatom (k,1.54d0,109.5d0,107.8d0,cai,ni,ci,chiral(i)) call zatom (k+2,1.50d0,109.5d0,chi(1,i),n-1,cai,ni,0) call zatom (k+3,1.39d0,120.0d0,chi(2,i),n-1,n-2,cai,0) call zatom (k+3,1.39d0,120.0d0,120.0d0,n-2,n-3,n-1,1) call zatom (k+5,1.39d0,120.0d0,180.0d0,n-2,n-3,n-4,0) call zatom (k+5,1.39d0,120.0d0,180.0d0,n-2,n-4,n-5,0) call zatom (k+7,1.39d0,120.0d0,0.0d0,n-2,n-4,n-5,0) call zatom (-1,0.0d0,0.0d0,0.0d0,n-2,n-1,0,0) call zatom (k+8,1.36d0,120.0d0,120.0d0,n-1,n-2,n-3,1) call zatom (k+1,1.11d0,109.4d0,109.4d0,n-8,cai,n-7,1) call zatom (k+1,1.11d0,109.4d0,109.4d0,n-9,cai,n-8,-1) call zatom (k+4,1.10d0,120.0d0,120.0d0,n-8,n-9,n-6,1) call zatom (k+4,1.10d0,120.0d0,120.0d0,n-8,n-10,n-6,1) call zatom (k+6,1.10d0,120.0d0,120.0d0,n-8,n-10,n-6,1) call zatom (k+6,1.10d0,120.0d0,120.0d0,n-8,n-10,n-7,1) c c tryptophan residue (TRP) c else if (resname .eq. 'TRP') then call zatom (k,1.54d0,109.5d0,109.5d0,cai,ni,ci,chiral(i)) call zatom (k+2,1.50d0,109.5d0,chi(1,i),n-1,cai,ni,0) call zatom (k+3,1.35d0,126.0d0,chi(2,i),n-1,n-2,cai,0) call zatom (k+5,1.35d0,126.0d0,108.0d0,n-2,n-3,n-1,1) call zatom (k+6,1.35d0,108.0d0,0.0d0,n-2,n-3,n-1,0) call zatom (k+8,1.35d0,108.0d0,0.0d0,n-1,n-3,n-4,0) call zatom (-1,0.0d0,0.0d0,0.0d0,n-3,n-1,0,0) call zatom (k+9,1.35d0,120.0d0,180.0d0,n-3,n-1,n-2,0) call zatom (k+11,1.35d0,120.0d0,0.0d0,n-2,n-4,n-1,0) call zatom (k+13,1.35d0,120.0d0,0.0d0,n-2,n-5,n-3,0) call zatom (k+15,1.35d0,120.0d0,0.0d0,n-2,n-4,n-6,0) call zatom (-1,0.0d0,0.0d0,0.0d0,n-2,n-1,0,0) call zatom (k+1,1.11d0,109.4d0,109.4d0,n-10,cai,n-9,1) call zatom (k+1,1.11d0,109.4d0,109.4d0,n-11,cai,n-10,-1) call zatom (k+4,1.10d0,126.0d0,126.0d0,n-10,n-11,n-8,1) call zatom (k+7,1.05d0,126.0d0,126.0d0,n-9,n-11,n-8,1) call zatom (k+10,1.10d0,120.0d0,120.0d0,n-8,n-11,n-6,1) call zatom (k+12,1.10d0,120.0d0,120.0d0,n-8,n-10,n-6,1) call zatom (k+14,1.10d0,120.0d0,120.0d0,n-8,n-10,n-7,1) call zatom (k+16,1.10d0,120.0d0,120.0d0,n-8,n-10,n-9,1) c c histidine (HD and HE) residue (HIS) c else if (resname .eq. 'HIS') then call zatom (k,1.54d0,109.5d0,109.5d0,cai,ni,ci,chiral(i)) call zatom (k+2,1.50d0,109.5d0,chi(1,i),n-1,cai,ni,0) call zatom (k+3,1.35d0,126.0d0,chi(2,i),n-1,n-2,cai,0) call zatom (k+5,1.35d0,126.0d0,108.0d0,n-2,n-3,n-1,1) call zatom (k+7,1.35d0,108.0d0,0.0d0,n-2,n-3,n-1,0) call zatom (k+9,1.35d0,108.0d0,0.0d0,n-2,n-4,n-3,0) call zatom (-1,0.0d0,0.0d0,.00d0,n-2,n-1,0,0) call zatom (k+1,1.11d0,109.4d0,109.4d0,n-6,cai,n-5,1) call zatom (k+1,1.11d0,109.4d0,109.4d0,n-7,cai,n-6,-1) call zatom (k+4,1.02d0,126.0d0,0.0d0,n-6,n-7,n-8,0) call zatom (k+6,1.10d0,126.0d0,126.0d0,n-6,n-8,n-4,1) call zatom (k+8,1.10d0,126.0d0,126.0d0,n-6,n-8,n-5,1) call zatom (k+10,1.02d0,126.0d0,126.0d0,n-6,n-8,n-7,1) c c histidine (HD only) residue (HID) c else if (resname .eq. 'HID') then call zatom (k,1.54d0,109.5d0,109.5d0,cai,ni,ci,chiral(i)) call zatom (k+2,1.50d0,109.5d0,chi(1,i),n-1,cai,ni,0) call zatom (k+3,1.35d0,126.0d0,chi(2,i),n-1,n-2,cai,0) call zatom (k+5,1.35d0,126.0d0,108.0d0,n-2,n-3,n-1,1) call zatom (k+7,1.35d0,108.0d0,0.0d0,n-2,n-3,n-1,0) call zatom (k+9,1.35d0,108.0d0,0.0d0,n-2,n-4,n-3,0) call zatom (-1,0.0d0,0.0d0,.00d0,n-2,n-1,0,0) call zatom (k+1,1.11d0,109.4d0,109.4d0,n-6,cai,n-5,1) call zatom (k+1,1.11d0,109.4d0,109.4d0,n-7,cai,n-6,-1) call zatom (k+4,1.02d0,126.0d0,0.0d0,n-6,n-7,n-8,0) call zatom (k+6,1.10d0,126.0d0,126.0d0,n-6,n-8,n-4,1) call zatom (k+8,1.10d0,126.0d0,126.0d0,n-6,n-8,n-5,1) c c histidine (HE only) residue (HIE) c else if (resname .eq. 'HIE') then call zatom (k,1.54d0,109.5d0,109.5d0,cai,ni,ci,chiral(i)) call zatom (k+2,1.50d0,109.5d0,chi(1,i),n-1,cai,ni,0) call zatom (k+3,1.35d0,126.0d0,chi(2,i),n-1,n-2,cai,0) call zatom (k+4,1.35d0,126.0d0,108.0d0,n-2,n-3,n-1,1) call zatom (k+6,1.35d0,108.0d0,0.0d0,n-2,n-3,n-1,0) call zatom (k+8,1.35d0,108.0d0,0.0d0,n-2,n-4,n-3,0) call zatom (-1,0.0d0,0.0d0,.00d0,n-2,n-1,0,0) call zatom (k+1,1.11d0,109.4d0,109.4d0,n-6,cai,n-5,1) call zatom (k+1,1.11d0,109.4d0,109.4d0,n-7,cai,n-6,-1) call zatom (k+5,1.10d0,126.0d0,126.0d0,n-5,n-7,n-3,1) call zatom (k+7,1.10d0,126.0d0,126.0d0,n-5,n-7,n-4,1) call zatom (k+9,1.02d0,126.0d0,126.0d0,n-5,n-7,n-6,1) c c aspartate residue (ASP) c else if (resname .eq. 'ASP') then call zatom (k,1.54d0,109.5d0,107.8d0,cai,ni,ci,chiral(i)) call zatom (k+2,1.51d0,107.8d0,chi(1,i),n-1,cai,ni,0) call zatom (k+3,1.25d0,117.0d0,chi(2,i),n-1,n-2,cai,0) call zatom (k+3,1.25d0,117.0d0,126.0d0,n-2,n-3,n-1,1) call zatom (k+1,1.11d0,109.4d0,107.9d0,n-4,cai,n-3,1) call zatom (k+1,1.11d0,109.4d0,107.9d0,n-5,cai,n-4,-1) c c protonated aspartic acid residue (ASH) c else if (resname .eq. 'ASH') then call zatom (k,1.54d0,109.5d0,107.8d0,cai,ni,ci,chiral(i)) call zatom (k+2,1.51d0,107.8d0,chi(1,i),n-1,cai,ni,0) call zatom (k+3,1.25d0,117.0d0,chi(2,i),n-1,n-2,cai,0) call zatom (k+4,1.40d0,117.0d0,126.0d0,n-2,n-3,n-1,1) call zatom (k+1,1.11d0,109.4d0,107.9d0,n-4,cai,n-3,1) call zatom (k+1,1.11d0,109.4d0,107.9d0,n-5,cai,n-4,-1) call zatom (k+5,0.98d0,108.7d0,0.0d0,n-3,n-5,n-4,0) c c asparagine residue (ASN) c else if (resname .eq. 'ASN') then call zatom (k,1.54d0,109.5d0,107.8d0,cai,ni,ci,chiral(i)) call zatom (k+2,1.51d0,107.8d0,chi(1,i),n-1,cai,ni,0) call zatom (k+3,1.22d0,122.5d0,chi(2,i),n-1,n-2,cai,0) call zatom (k+4,1.34d0,112.7d0,124.0d0,n-2,n-3,n-1,1) call zatom (k+1,1.11d0,109.4d0,107.9d0,n-4,cai,n-3,1) call zatom (k+1,1.11d0,109.4d0,107.9d0,n-5,cai,n-4,-1) call zatom (k+5,1.02d0,119.0d0,0.0d0,n-3,n-5,n-6,0) call zatom (k+5,1.02d0,119.0d0,120.0d0,n-4,n-6,n-1,1) c c glutamate residue (GLU) c else if (resname .eq. 'GLU') then call zatom (k,1.54d0,109.5d0,107.8d0,cai,ni,ci,chiral(i)) call zatom (k+2,1.54d0,109.5d0,chi(1,i),n-1,cai,ni,0) call zatom (k+4,1.51d0,107.8d0,chi(2,i),n-1,n-2,cai,0) call zatom (k+5,1.25d0,117.0d0,chi(3,i),n-1,n-2,n-3,0) call zatom (k+5,1.25d0,117.0d0,126.0d0,n-2,n-3,n-1,1) call zatom (k+1,1.11d0,109.4d0,109.4d0,n-5,cai,n-4,1) call zatom (k+1,1.11d0,109.4d0,109.4d0,n-6,cai,n-5,-1) call zatom (k+3,1.11d0,109.4d0,107.9d0,n-6,n-7,n-5,1) call zatom (k+3,1.11d0,109.4d0,107.9d0,n-7,n-8,n-6,-1) c c protonated glutamic acid residue (GLH) c else if (resname .eq. 'GLH') then call zatom (k,1.54d0,109.5d0,107.8d0,cai,ni,ci,chiral(i)) call zatom (k+2,1.54d0,109.5d0,chi(1,i),n-1,cai,ni,0) call zatom (k+4,1.51d0,107.8d0,chi(2,i),n-1,n-2,cai,0) call zatom (k+5,1.25d0,117.0d0,chi(3,i),n-1,n-2,n-3,0) call zatom (k+6,1.40d0,117.0d0,126.0d0,n-2,n-3,n-1,1) call zatom (k+1,1.11d0,109.4d0,109.4d0,n-5,cai,n-4,1) call zatom (k+1,1.11d0,109.4d0,109.4d0,n-6,cai,n-5,-1) call zatom (k+3,1.11d0,109.4d0,107.9d0,n-6,n-7,n-5,1) call zatom (k+3,1.11d0,109.4d0,107.9d0,n-7,n-8,n-6,-1) call zatom (k+7,0.98d0,108.7d0,0.0d0,n-5,n-7,n-6,0) c c glutamine residue (GLN) c else if (resname .eq. 'GLN') then call zatom (k,1.54d0,109.5d0,107.8d0,cai,ni,ci,chiral(i)) call zatom (k+2,1.54d0,109.5d0,chi(1,i),n-1,cai,ni,0) call zatom (k+4,1.51d0,107.8d0,chi(2,i),n-1,n-2,cai,0) call zatom (k+5,1.22d0,122.5d0,chi(3,i),n-1,n-2,n-3,0) call zatom (k+6,1.34d0,112.7d0,124.0d0,n-2,n-3,n-1,1) call zatom (k+1,1.11d0,109.4d0,109.4d0,n-5,cai,n-4,1) call zatom (k+1,1.11d0,109.4d0,109.4d0,n-6,cai,n-5,-1) call zatom (k+3,1.11d0,109.4d0,107.9d0,n-6,n-7,n-5,1) call zatom (k+3,1.11d0,109.4d0,107.9d0,n-7,n-8,n-6,-1) call zatom (k+7,1.02d0,119.0d0,0.0d0,n-5,n-7,n-8,0) call zatom (k+7,1.02d0,119.0d0,120.0d0,n-6,n-8,n-1,1) c c methionine residue (MET) c else if (resname .eq. 'MET') then call zatom (k,1.54d0,109.5d0,107.8d0,cai,ni,ci,chiral(i)) call zatom (k+2,1.54d0,109.5d0,chi(1,i),n-1,cai,ni,0) call zatom (k+4,1.82d0,109.0d0,chi(2,i),n-1,n-2,cai,0) call zatom (k+5,1.82d0,96.3d0,chi(3,i),n-1,n-2,n-3,0) call zatom (k+1,1.11d0,109.4d0,109.4d0,n-4,cai,n-3,1) call zatom (k+1,1.11d0,109.4d0,109.4d0,n-5,cai,n-4,-1) call zatom (k+3,1.11d0,109.4d0,112.0d0,n-5,n-6,n-4,1) call zatom (k+3,1.11d0,109.4d0,112.0d0,n-6,n-7,n-5,-1) call zatom (k+6,1.11d0,112.0d0,180.0d0,n-5,n-6,n-7,0) call zatom (k+6,1.11d0,112.0d0,109.4d0,n-6,n-7,n-1,1) call zatom (k+6,1.11d0,112.0d0,109.4d0,n-7,n-8,n-2,-1) c c lysine residue (LYS) c else if (resname .eq. 'LYS') then call zatom (k,1.54d0,109.5d0,107.8d0,cai,ni,ci,chiral(i)) call zatom (k+2,1.54d0,109.5d0,chi(1,i),n-1,cai,ni,0) call zatom (k+4,1.54d0,109.5d0,chi(2,i),n-1,n-2,cai,0) call zatom (k+6,1.54d0,109.5d0,chi(3,i),n-1,n-2,n-3,0) call zatom (k+8,1.50d0,109.5d0,chi(4,i),n-1,n-2,n-3,0) call zatom (k+1,1.11d0,109.4d0,109.4d0,n-5,cai,n-4,1) call zatom (k+1,1.11d0,109.4d0,109.4d0,n-6,cai,n-5,-1) call zatom (k+3,1.11d0,109.4d0,109.4d0,n-6,n-7,n-5,1) call zatom (k+3,1.11d0,109.4d0,109.4d0,n-7,n-8,n-6,-1) call zatom (k+5,1.11d0,109.4d0,109.4d0,n-7,n-8,n-6,1) call zatom (k+5,1.11d0,109.4d0,109.4d0,n-8,n-9,n-7,-1) call zatom (k+7,1.11d0,109.4d0,108.8d0,n-8,n-9,n-7,1) call zatom (k+7,1.11d0,109.4d0,108.8d0,n-9,n-10,n-8,-1) call zatom (k+9,1.02d0,109.5d0,180.0d0,n-9,n-10,n-11,0) call zatom (k+9,1.02d0,109.5d0,109.5d0,n-10,n-11,n-1,1) call zatom (k+9,1.02d0,109.5d0,109.5d0,n-11,n-12,n-2,-1) c c deprotonated lysine residue (LYD) c else if (resname .eq. 'LYD') then call zatom (k,1.54d0,109.5d0,107.8d0,cai,ni,ci,chiral(i)) call zatom (k+2,1.54d0,109.5d0,chi(1,i),n-1,cai,ni,0) call zatom (k+4,1.54d0,109.5d0,chi(2,i),n-1,n-2,cai,0) call zatom (k+6,1.54d0,109.5d0,chi(3,i),n-1,n-2,n-3,0) call zatom (k+8,1.50d0,109.5d0,chi(4,i),n-1,n-2,n-3,0) call zatom (k+1,1.11d0,109.4d0,109.4d0,n-5,cai,n-4,1) call zatom (k+1,1.11d0,109.4d0,109.4d0,n-6,cai,n-5,-1) call zatom (k+3,1.11d0,109.4d0,109.4d0,n-6,n-7,n-5,1) call zatom (k+3,1.11d0,109.4d0,109.4d0,n-7,n-8,n-6,-1) call zatom (k+5,1.11d0,109.4d0,109.4d0,n-7,n-8,n-6,1) call zatom (k+5,1.11d0,109.4d0,109.4d0,n-8,n-9,n-7,-1) call zatom (k+7,1.11d0,109.4d0,108.8d0,n-8,n-9,n-7,1) call zatom (k+7,1.11d0,109.4d0,108.8d0,n-9,n-10,n-8,-1) call zatom (k+9,1.02d0,109.5d0,180.0d0,n-9,n-10,n-11,0) call zatom (k+9,1.02d0,109.5d0,109.5d0,n-10,n-11,n-1,1) c c arginine residue (ARG) c else if (resname .eq. 'ARG') then call zatom (k,1.54d0,109.5d0,107.8d0,cai,ni,ci,chiral(i)) call zatom (k+2,1.54d0,109.5d0,chi(1,i),n-1,cai,ni,0) call zatom (k+4,1.54d0,109.5d0,chi(2,i),n-1,n-2,cai,0) call zatom (k+6,1.45d0,109.5d0,chi(3,i),n-1,n-2,n-3,0) call zatom (k+8,1.35d0,120.0d0,chi(4,i),n-1,n-2,n-3,0) call zatom (k+9,1.35d0,120.0d0,180.0d0,n-1,n-2,n-3,0) call zatom (k+9,1.35d0,120.0d0,120.0d0,n-2,n-3,n-1,1) call zatom (k+1,1.11d0,109.4d0,109.4d0,n-7,cai,n-6,1) call zatom (k+1,1.11d0,109.4d0,109.4d0,n-8,cai,n-7,-1) call zatom (k+3,1.11d0,109.4d0,109.4d0,n-8,n-9,n-7,1) call zatom (k+3,1.11d0,109.4d0,109.4d0,n-9,n-10,n-8,-1) call zatom (k+5,1.11d0,109.4d0,109.4d0,n-9,n-10,n-8,1) call zatom (k+5,1.11d0,109.4d0,109.4d0,n-10,n-11,n-9,-1) call zatom (k+7,1.02d0,120.0d0,120.0d0,n-10,n-11,n-9,1) call zatom (k+10,1.02d0,120.0d0,180.0d0,n-9,n-10,n-11,0) call zatom (k+10,1.02d0,120.0d0,120.0d0,n-10,n-11,n-1,1) call zatom (k+10,1.02d0,120.0d0,180.0d0,n-10,n-12,n-13,0) call zatom (k+10,1.02d0,120.0d0,120.0d0,n-11,n-13,n-1,1) c c ornithine residue (ORN) c else if (resname .eq. 'ORN') then call zatom (k,1.54d0,109.5d0,107.8d0,cai,ni,ci,chiral(i)) call zatom (k+2,1.54d0,109.5d0,chi(1,i),n-1,cai,ni,0) call zatom (k+4,1.54d0,109.5d0,chi(2,i),n-1,n-2,cai,0) call zatom (k+6,1.50d0,109.5d0,chi(3,i),n-1,n-2,n-3,0) call zatom (k+1,1.11d0,109.4d0,109.4d0,n-4,cai,n-3,1) call zatom (k+1,1.11d0,109.4d0,109.4d0,n-5,cai,n-4,-1) call zatom (k+3,1.11d0,109.4d0,109.4d0,n-5,n-6,n-4,1) call zatom (k+3,1.11d0,109.4d0,109.4d0,n-6,n-7,n-5,-1) call zatom (k+5,1.11d0,109.4d0,109.4d0,n-6,n-7,n-5,1) call zatom (k+5,1.11d0,109.4d0,109.4d0,n-7,n-8,n-6,-1) call zatom (k+7,1.02d0,109.5d0,180.0d0,n-7,n-8,n-9,0) call zatom (k+7,1.02d0,109.5d0,109.5d0,n-8,n-9,n-1,1) call zatom (k+7,1.02d0,109.5d0,109.5d0,n-9,n-10,n-2,-1) c c methylalanine residue (AIB) c else if (resname .eq. 'AIB') then call zatom (k,1.54d0,109.5d0,107.8d0,cai,ni,ci,-chiral(i)) call zatom (k,1.54d0,109.5d0,107.8d0,cai,ni,ci,chiral(i)) call zatom (k+1,1.11d0,109.4d0,chi(1,i),n-2,cai,ni,0) call zatom (k+1,1.11d0,109.4d0,109.4d0,n-3,cai,n-1,1) call zatom (k+1,1.11d0,109.4d0,109.4d0,n-4,cai,n-2,-1) call zatom (k+1,1.11d0,109.4d0,chi(1,i),n-4,cai,ni,0) call zatom (k+1,1.11d0,109.4d0,109.4d0,n-5,cai,n-1,1) call zatom (k+1,1.11d0,109.4d0,109.4d0,n-6,cai,n-2,-1) c c pyroglutamic acid residue (PCA) c else if (resname .eq. 'PCA') then call zatom (k,1.54d0,107.0d0,109.5d0,cai,ni,ci,chiral(i)) call zatom (k+2,1.54d0,107.0d0,chi(1,i),n-1,cai,ni,0) call zatom (k+4,1.54d0,107.0d0,chi(2,i),n-1,n-2,cai,0) call zatom (-1,0.0d0,0.0d0,0.0d0,ni,n-1,0,0) call zatom (k+5,1.22d0,126.0d0,126.0d0,n-1,ni,n-2,1) call zatom (k+1,1.11d0,109.4d0,109.4d0,n-4,cai,n-3,1) call zatom (k+1,1.11d0,109.4d0,109.4d0,n-5,cai,n-4,-1) call zatom (k+3,1.11d0,109.4d0,109.4d0,n-5,n-6,n-4,1) call zatom (k+3,1.11d0,109.4d0,109.4d0,n-6,n-7,n-5,-1) c c unknown residue (UNK) c else if (resname .eq. 'UNK') then k = hatyp(seqtyp(i)) if (i .eq. 1) k = hantyp(seqtyp(i)) if (i .eq. nseq) k = hactyp(seqtyp(i)) call zatom (k,1.11d0,109.5d0,107.9d0,cai,ni,ci,chiral(i)) end if return end c c c ################################################################ c ## ## c ## subroutine pauling -- pack multiple polypeptide chains ## c ## ## c ################################################################ c c c "pauling" uses a rigid body optimization to approximately c pack multiple polypeptide chains c c subroutine pauling use atomid use atoms use couple use group use inform use katoms use molcul use output use potent use restrn use rigid use usage implicit none integer i,j,k,nvar real*8 minimum,grdmin real*8 pauling1 real*8, allocatable :: xx(:) external pauling1,optsave c c c perform dynamic allocation of some global arrays c if (.not. allocated(iuse)) allocate (iuse(n)) if (.not. allocated(use)) allocate (use(0:n)) c c set all atoms to be active during energy evaluations c nuse = n do i = 1, n use(i) = .true. end do c c only geometric restraints will by used in optimization c call potoff use_geom = .true. c c set the default values for the restraint variables c npfix = 0 ndfix = 0 ntfix = 0 ngfix = 0 nchir = 0 use_basin = .true. depth = 3.0d0 width = 1.5d0 use_wall = .false. c c enable use of groups based on number of molecules c use_group = .true. ngrp = nmol c c perform dynamic allocation of some global arrays c if (.not. allocated(kgrp)) allocate (kgrp(n)) if (.not. allocated(grplist)) allocate (grplist(n)) if (.not. allocated(igrp)) allocate (igrp(2,0:ngrp)) if (.not. allocated(grpmass)) allocate (grpmass(0:ngrp)) if (.not. allocated(wgrp)) allocate (wgrp(0:ngrp,0:ngrp)) c c assign each chain to a separate molecule-based group c do i = 1, ngrp igrp(1,i) = imol(1,i) igrp(2,i) = imol(2,i) do j = igrp(1,i), igrp(2,i) kgrp(j) = kmol(j) grplist(kgrp(j)) = i end do end do do i = 0, ngrp do j = 0, ngrp wgrp(j,i) = 1.0d0 end do wgrp(i,i) = 1.0d0 end do c c assume unit mass for each atom and set group masses c do i = 1, n mass(i) = 1.0d0 end do do i = 1, ngrp grpmass(i) = dble(igrp(2,i)-igrp(1,i)+1) end do c c perform dynamic allocation of some global arrays c maxfix = max(n,ngrp*ngrp) if (allocated(ipfix)) deallocate(ipfix) if (allocated(kpfix)) deallocate(kpfix) if (allocated(xpfix)) deallocate(xpfix) if (allocated(ypfix)) deallocate(ypfix) if (allocated(zpfix)) deallocate(zpfix) if (allocated(pfix)) deallocate(pfix) if (allocated(igfix)) deallocate(igfix) if (allocated(gfix)) deallocate(gfix) allocate (ipfix(maxfix)) allocate (kpfix(3,maxfix)) allocate (xpfix(maxfix)) allocate (ypfix(maxfix)) allocate (zpfix(maxfix)) allocate (pfix(2,maxfix)) allocate (igfix(2,maxfix)) allocate (gfix(3,maxfix)) c c set position restraints on alpha carbons of each chain c do i = 1, n if (atmnum(type(i)) .eq. 6) then do j = 1, n12(i) if (atmnum(type(i12(j,i))) .eq. 7) then do k = 1, n13(i) if (atmnum(type(i13(k,i))) .eq. 8) then npfix = npfix + 1 ipfix(npfix) = i kpfix(1,npfix) = 1 kpfix(2,npfix) = 1 kpfix(3,npfix) = 0 xpfix(npfix) = 11.0d0 * dble(grplist(i)-1) ypfix(npfix) = 0.0d0 zpfix(npfix) = 0.0d0 pfix(1,npfix) = 1.0d0 pfix(2,npfix) = 0.0d0 goto 10 end if end do end if end do end if 10 continue end do c c set pairwise restraints between the centers of chains c do i = 1, ngrp-1 do j = i+1, ngrp ngfix = ngfix + 1 igfix(1,ngfix) = i igfix(2,ngfix) = j gfix(1,ngfix) = 1.0d0 gfix(2,ngfix) = 11.0d0 * dble(j-i) gfix(3,ngfix) = 11.0d0 * dble(j-i) end do end do c c get rigid body reference coordinates for each chain c call orient c c perform dynamic allocation of some local arrays c allocate (xx(6*ngrp)) c c convert rigid body coordinates to optimization parameters c nvar = 0 do i = 1, ngrp do j = 1, 6 nvar = nvar + 1 xx(nvar) = rbc(j,i) end do end do c c make the call to the optimization routine c iprint = 0 iwrite = 0 grdmin = 0.1d0 coordtype = 'NONE' call ocvm (nvar,xx,minimum,grdmin,pauling1,optsave) c c convert optimization parameters to rigid body coordinates c nvar = 0 do i = 1, ngrp do j = 1, 6 nvar = nvar + 1 rbc(j,i) = xx(nvar) end do end do c c perform deallocation of some local arrays c deallocate (xx) c c convert from rigid body to Cartesian coordinates c call rigidxyz return end c c c ############################################################## c ## ## c ## function pauling1 -- energy and gradient for pauling ## c ## ## c ############################################################## c c c "pauling1" is a service routine that computes the energy c and gradient for optimally conditioned variable metric c optimization of rigid bodies c c function pauling1 (xx,g) use group use math use rigid implicit none integer i,j,nvar real*8 pauling1,e real*8 xx(*) real*8 g(*) real*8, allocatable :: derivs(:,:) c c c convert optimization parameters to rigid body coordinates c nvar = 0 do i = 1, ngrp do j = 1, 6 nvar = nvar + 1 rbc(j,i) = xx(nvar) end do end do c c perform dynamic allocation of some local arrays c allocate (derivs(6,ngrp)) c c compute and store the energy and gradient c call rigidxyz call gradrgd (e,derivs) pauling1 = e c c convert gradient components to optimization parameters c nvar = 0 do i = 1, ngrp do j = 1, 6 nvar = nvar + 1 g(nvar) = derivs(j,i) end do end do c c perform deallocation of some local arrays c deallocate (derivs) return end