def writepdb(mol, atids, fname):
wf = open(fname, 'w')
print >> wf, 'REMARK, BUILD BY MCPB.PY'
resids = []
for i in atids:
if mol.atoms[i].resid not in resids:
resids.append(mol.atoms[i].resid)
reslist = get_reslist(mol, resids)
terlist = reslist.nterm + reslist.nonstd + reslist.water
terlist = list(set(terlist))
for i in resids:
if (i in terlist) and (i != min(resids)):
print >> wf, 'TER'
for j in mol.residues[i].resconter:
atm = mol.atoms[j]
gtype = atm.gtype
atid = atm.atid
if len(atm.atname) == 3:
atname = atm.atname
else:
atname = atm.atname.center(4)
crd = atm.crd
resid = atm.resid
resname = mol.residues[resid].resname
print >> wf, "%-6s%5d %4s %3s %1s%4d %8.3f%8.3f%8.3f%6.2f%6.2f" \
%(gtype, atid, atname, resname, 'A', resid, crd[0], crd[1], crd[2], 1.00, 0.00)
print >> wf, 'END'
wf.close()
def writepdb(mol, atids, fname):
wf = open(fname, 'w')
print >> wf, 'REMARK, BUILD BY MCPB.PY'
resids = []
for i in atids:
if mol.atoms[i].resid not in resids:
resids.append(mol.atoms[i].resid)
reslist = get_reslist(mol, resids)
terlist = reslist.nterm + reslist.nonstd + reslist.water
terlist = list(set(terlist))
for i in resids:
if (i in terlist) and (i != min(resids)):
print >> wf, 'TER'
for j in mol.residues[i].resconter:
atm = mol.atoms[j]
gtype = atm.gtype
atid = atm.atid
if len(atm.atname) == 3:
atname = atm.atname
else:
atname = atm.atname.center(4)
crd = atm.crd
resid = atm.resid
resname = mol.residues[resid].resname
print >> wf, "%-6s%5d %4s %3s %1s%4d %8.3f%8.3f%8.3f%6.2f%6.2f" \
%(gtype, atid, atname, resname, 'A', resid, crd[0], crd[1], crd[2], 1.00, 0.00)
print >> wf, 'END'
wf.close()
def gene_resp_input_file(lgpdbf, ionids, stfpf, ffchoice, mol2fs,
chgmod, fixchg_resids, lgchg):
libdict, chargedict = get_lib_dict(ffchoice)
for mol2f in mol2fs:
libdict1, chargedict1 = get_lib_dict(mol2f)
libdict.update(libdict1)
chargedict.update(chargedict1)
mol, atids, resids = get_atominfo_fpdb(lgpdbf)
reslist = get_reslist(mol, resids)
blist = get_mc_blist(mol, atids, ionids, stfpf)
bnoatids = [] #Binding backbone N and C Atom IDs
mcresids = [] #Metal site residues
stfpff = open(stfpf, 'r')
for line in stfpff:
if line[0:4] != 'LINK':
line = line.split()
line = line[0].split('-')
mcresids.append(int(line[0]))
else:
line = line.strip('\n')
line = line.split()
if (line[-1][-1] in ['N3', 'N', 'O', 'OXT']):
atid, atom = line[-1].split('-')
bnoatids.append(int(atid))
stfpff.close()
bnoresids = [] #Binding Backbone N and C Residue IDs, which are not fitted
#with backbone restriction in the charge fitting
for i in bnoatids:
resid = mol.atoms[i].resid
if resid not in bnoresids:
bnoresids.append(resid)
angresids = [] #ACE, NME, GLY residues
for i in resids:
if i not in mcresids:
angresids.append(i)
#Get the total charge of the system-------------------------------------
totchg = 0.0
for i in resids:
resname = mol.residues[i].resname
if i in reslist.nterm:
reschg = chargedict['N' + resname]
elif i in reslist.cterm:
reschg = chargedict['C' + resname]
else:
reschg = chargedict[resname]
totchg = totchg + reschg
totchg = int(round(totchg, 0))
if lgchg == -99:
lgchg = totchg
#-------------------------------------------------------------------------
##############RESP1.IN file###############################################
#-------------------------------------------------------------------------
print "***Generating the 1st stage resp charge fitting input file..."
#print the 1st part, the title
fresp1 = open('resp1.in', 'w')
print >> fresp1, "Resp charges for organic molecule"
print >> fresp1, " "
print >> fresp1, " &cntrl"
print >> fresp1, " "
print >> fresp1, " nmol = 1,"
print >> fresp1, " ihfree = 1,"
print >> fresp1, " ioutopt = 1,"
print >> fresp1, " "
print >> fresp1, " &end"
print >> fresp1, " 1.0"
print >> fresp1, "Resp charges for organic molecule"
print >> fresp1, "%5d" %lgchg,
print >> fresp1, "%4d" %len(atids)
#2. print the 2nd part, the free and fozen atoms---------------------------
natids = [i for i in range(1, len(atids)+1)] #new atids
iddict = {} #First number in iddict is new atom id, second is atomic number
for i in range(0, len(atids)):
iddict[atids[i]] = natids[i]
for i in atids:
element = mol.atoms[i].element
elenum = Atnum[element]
iddict[i] = (iddict[i], elenum)
for i in resids:
get_equal_atoms(mol, i, blist, iddict)
#other atoms (except the CH2 and CH3 groups) are frozen
for i in atids:
if (len(iddict[i]) == 2):
iddict[i] = (iddict[i][0], iddict[i][1], -99)
for i in atids:
#if iddict[i][2] == -99:
print >> fresp1, "%5d" %iddict[i][1],
print >> fresp1, "%4s" %'0'
#else:
# print >> fresp1, "%5d" %iddict[i][1],
# print >> fresp1, "%4s" %iddict[i][2]
fresp1.close()
add_restriction('resp1.in', libdict, mol, resids, reslist, mcresids,
bnoresids, angresids, iddict, chgmod, fixchg_resids)
#-------------------------------------------------------------------------
####################RESP2.IN file#########################################
#-------------------------------------------------------------------------
print "***Generating the 2nd stage resp charge fitting input file..."
#1. print the 1st part, the title------------------------------------------
fresp2 = open('resp2.in', 'w')
print >> fresp2, "Resp charges for organic molecule"
print >> fresp2, " "
print >> fresp2, " &cntrl"
print >> fresp2, " "
print >> fresp2, " nmol = 1,"
print >> fresp2, " ihfree = 1,"
print >> fresp2, " ioutopt = 1,"
print >> fresp2, " iqopt = 2,"
print >> fresp2, " qwt = 0.001,"
print >> fresp2, " "
print >> fresp2, " &end"
print >> fresp2, " 1.0"
print >> fresp2, "Resp charges for organic molecule"
print >> fresp2, "%5d" %lgchg,
print >> fresp2, "%4d" %len(atids)
#2. print the 2nd part, the free or frozen information---------------------
for i in atids:
print >> fresp2, "%5d" %iddict[i][1],
print >> fresp2, "%4s" %iddict[i][2]
fresp2.close()
add_restriction('resp2.in', libdict, mol, resids, reslist, mcresids,
bnoresids, angresids, iddict, chgmod, fixchg_resids)
def rename_res(mol, atids):
#Residue IDs
resids = []
for i in atids:
if mol.atoms[i].resid not in resids:
resids.append(mol.atoms[i].resid)
#Correct the names of the HIS, ASP, GLU, LYS, CYS
for i in resids:
#HIS
if mol.residues[i].resname == 'HIS':
hasatoms = []
for j in mol.residues[i].resconter:
atname = mol.atoms[j].atname
hasatoms.append(atname)
if ('HD1' in hasatoms) and ('HE2' in hasatoms):
mol.residues[i].resname = 'HIP'
elif ('HD1' in hasatoms):
mol.residues[i].resname = 'HID'
elif ('HE2' in hasatoms):
mol.residues[i].resname = 'HIE'
#ASP
elif mol.residues[i].resname == 'ASP':
hasatoms = []
for j in mol.residues[i].resconter:
atname = mol.atoms[j].atname
hasatoms.append(atname)
if ('HD1' in hasatoms) or ('HD2' in hasatoms):
mol.residues[i].resname = 'ASH'
#GLU
elif mol.residues[i].resname == 'GLU':
hasatoms = []
for j in mol.residues[i].resconter:
atname = mol.atoms[j].atname
hasatoms.append(atname)
if ('HE1' in hasatoms) or ('HE2' in hasatoms):
mol.residues[i].resname = 'GLH'
#LYS
elif mol.residues[i].resname == 'LYS':
hasatoms = []
for j in mol.residues[i].resconter:
atname = mol.atoms[j].atname
hasatoms.append(atname)
if ('HZ1' not in hasatoms):
mol.residues[i].resname = 'LYN'
#CYS
elif mol.residues[i].resname == 'CYS':
hasatoms = []
for j in mol.residues[i].resconter:
atname = mol.atoms[j].atname
hasatoms.append(atname)
if ('HG' not in hasatoms): ##There are two different situations
#for atom in CYS residue
for j in mol.residues[i].resconter:
if mol.atoms[j].atname == 'SG':
sgcrd = mol.atoms[j].crd
#for every atom
for k in atids:
if mol.atoms[k].atname == 'SG' and k != j:
atkcrd = mol.atoms[k].crd
dis = calc_bond(sgcrd, atkcrd)
if dis <= 2.50:
mol.residues[i].resname = 'CYX'
else:
mol.residues[i].resname = 'CYM'
reslist = get_reslist(mol, resids)
#rename the HN atom to H atom in amino acid residues
for i in resids:
if i in reslist.std:
for j in mol.residues[i].resconter:
if mol.atoms[j].atname == 'HN':
mol.atoms[j].atname = 'H'
return mol
def gene_leaprc(gname, orpdbf, fipdbf, stpdbf, stfpf, ionids,\
ionmol2fs, ioninf, mcresname, naamol2fs, ff_choice, frcmodfs,
finfcdf, ileapf, model, watermodel='tip3p', paraset='cm'):
print "******************************************************************"
print "* *"
print "*=================Generating input file for leap=================*"
print "* *"
print "******************************************************************"
#---------------------Generate the new pdb file--------------------------
#mol0 is the old mol while mol is new mol file with new names
mol0, atids0, resids0 = get_atominfo_fpdb(orpdbf)
reslist0 = get_reslist(mol0, resids0)
mol, atids, resids = get_atominfo_fpdb(orpdbf)
#rename the residue names into AMBER style, e.g. HIS --> HID, HIP, HIE
mol = rename_res(mol, atids)
#get the disulfur bond information
disul = get_diS_bond(mol, atids)
#resname the old residue names to new ones if it is not metal ion
if model in [1, 2]:
metcenres1 = [] #Old residue ids
fp = open(stfpf, 'r')
for line in fp:
if line[0:4] != "LINK":
line = line.split('-')
if int(line[0]) not in metcenres1:
metcenres1.append(int(line[0]))
fp.close()
metcenres2 = mcresname #New residue names
resndict = {}
resns = []
for i in range(0, len(metcenres1)):
resndict[metcenres1[i]] = metcenres2[i]
resns.append(metcenres2[i])
for i in resndict.keys():
mol.residues[i].resname = resndict[i]
writepdb(mol, atids, fipdbf)
#----------------------------get the atom names which changed atom type
if model in [1, 2]:
atomdefs = {}
fp0 = open(stfpf, 'r')
for line in fp0:
if line[0:4] != "LINK":
line = line.strip('\n')
line = line.split()
if line[2] != line[4]:
atnewtype = line[4]
element = mol.atoms[int(line[1])].element
if atnewtype not in atomdefs.keys():
atomdefs[atnewtype] = element
else:
if element != atomdefs[atnewtype]:
raise pymsmtError('There are atoms in fingerprint file '
'of standard model with same atom type '
'but different element.')
fp0.close()
#---------------------Get the bond information, mol2 is the standard model
if model == 1:
mol2, atids2, resids2 = get_atominfo_fpdb(stpdbf)
blist = get_mc_blist(mol2, atids2, ionids, stfpf)
blist1 = [(i[0], i[1]) for i in blist]
#----------------------Generate the lib file and get the frcmod file name
if model == 2:
frcmodfs = []
for ionmol2f in ionmol2fs:
ionmol, ionatids, ionresids = get_atominfo(ionmol2f)
for i in ionatids:
element = ionmol.atoms[i].element
chg = int(ionmol.atoms[i].charge)
frcmodf = get_frcmod_fname(element, chg, watermodel, paraset)
if frcmodf not in frcmodfs:
frcmodfs.append(frcmodf)
elif model == 3 and ioninf != []:
#get the metal information
metresns = ioninf[0::4]
metatns = ioninf[1::4]
metelmts = ioninf[2::4]
metelmts = [i[0] + i[1:].lower() for i in metelmts]
metchgs = ioninf[3::4]
metchgs = [int(i) for i in metchgs]
#check the charge of the metal ions
for metchg in metchgs:
if metchg < -1 or metchg > 4:
raise pymsmtError('Could not deal with atomic ion which has charge '
'less than -1 or bigger than +4.')
frcmodfs = []
for i in range(0, len(metresns)):
if metchgs[i] > 1: #if it is -1 or +1 ions, no need to create the lib file
gene_ion_libfile(metresns[i], metatns[i], metelmts[i], metchgs[i])
frcmodf = get_frcmod_fname(metelmts[i], metchgs[i], watermodel, paraset)
if frcmodf not in frcmodfs:
frcmodfs.append(frcmodf)
#-----------------------Generate the leap input file-----------------------
print 'Generating the leap input file...'
##Generate the tleap.in file
lp = open(ileapf, 'w')
if ff_choice in ['ff94', 'ff99', 'ff99SB', 'ff03', 'ff10']:
print >> lp, 'source oldff/leaprc.%s' %ff_choice
elif ff_choice in ['ff03.r1', 'ff12SB', 'ff14SB']:
print >> lp, 'source leaprc.%s' %ff_choice
print >> lp, 'source leaprc.gaff'
#Add atom types, for bonded model
if model in [1, 2]:
if atomdefs.keys() != []:
print >> lp, 'addAtomTypes {'
for i in atomdefs.keys():
print >> lp, ' { "%s" "%s" "sp3" }' %(i, atomdefs[i])
print >> lp, '}'
#load lib and frcmod files for monovalent ions (for salt)
if ff_choice in ['ff94', 'ff99', 'ff99SB', 'ff03', 'ff03.r1']:
print >> lp, 'loadoff atomic_ions.lib'
print >> lp, 'loadamberparams frcmod.ions1lsm_hfe_%s' %watermodel
#Load mol2 file for the refitting charge residues
if model in [1, 2]:
for i in resns:
print >> lp, '%s = loadmol2 %s.mol2' %(i, i)
elif model == 3:
for i in naamol2fs:
print >> lp, '%s = loadmol2 %s.mol2' %(i, i)
#Load frcmod files for non-standard residues and metal site
for i in frcmodfs:
print >> lp, 'loadamberparams %s' %i
if model == 1:
print >> lp, 'loadamberparams %s' %finfcdf
elif model == 2:
for frcmodf in frcmodfs:
print >> lp, 'loadamberparams %s' %frcmodf
elif model == 3:
for metresn in metresns:
print >> lp, 'loadoff %s.lib' %metresn
for frcmodf in frcmodfs:
print >> lp, 'loadamberparams %s' %frcmodf
#load pdb file
print >> lp, 'mol = loadpdb %s' %fipdbf
##The Disulfur Bond information
if disul != []:
for i in disul:
at1 = i[0]
at2 = i[1]
resid1 = mol.atoms[at1].resid
resid2 = mol.atoms[at2].resid
atname1 = mol.atoms[at1].atname
atname2 = mol.atoms[at2].atname
print >> lp, 'bond', 'mol.' + str(resid1) + '.' + atname1, 'mol.' + \
str(resid2) + '.' + atname2
##Bond including the metal ions
if model == 1:
for bond in blist1:
if list(set(bond) & set(ionids)) != []:
at1 = bond[0]
at2 = bond[1]
resid1 = mol.atoms[at1].resid
resid2 = mol.atoms[at2].resid
atname1 = mol.atoms[at1].atname
atname2 = mol.atoms[at2].atname
print >> lp, 'bond', 'mol.' + str(resid1) + '.' + atname1, 'mol.' + \
str(resid2) + '.' + atname2
##Nonstandard residues with nearby residues
if model in [1, 2]:
bondcmds = []
for i in metcenres1:
resname = mol0.residues[i].resname
print 'Renamed residues includes: ' + str(i) + '-' + resname
if i in reslist0.nterm:
cmdi = 'bond mol.' + str(i) + '.C' + ' mol.' + str(i+i) + '.N'
if cmdi not in bondcmds:
bondcmds.append(cmdi)
elif i in reslist0.cterm:
cmdi = 'bond mol.' + str(i-1) + '.C' + ' mol.' + str(i) + '.N'
if cmdi not in bondcmds:
bondcmds.append(cmdi)
elif i in reslist0.std:
cmdi = 'bond mol.' + str(i-1) + '.C' + ' mol.' + str(i) + '.N'
if cmdi not in bondcmds:
bondcmds.append(cmdi)
cmdi = 'bond mol.' + str(i) + '.C' + ' mol.' + str(i+1) + '.N'
if cmdi not in bondcmds:
bondcmds.append(cmdi)
for j in bondcmds:
print >> lp, j
#Save dry structure
print >> lp, 'savepdb mol %s_dry.pdb' %gname
print >> lp, 'saveamberparm mol %s_dry.prmtop %s_dry.inpcrd' \
%(gname, gname)
#Solvatebox
if watermodel == 'tip3p':
print >> lp, 'solvatebox mol TIP3PBOX 10.0'
elif watermodel == 'spce':
print >> lp, 'solvatebox mol SPCBOX 10.0'
print >> lp, 'loadamberparams frcmod.spce'
elif watermodel == 'tip4pew':
print >> lp, 'solvatebox mol TIP4PEWBOX 10.0'
print >> lp, 'loadamberparams frcmod.tip4pew'
#Add counter ions
print >> lp, 'addions mol Na+ 0'
print >> lp, 'addions mol Cl- 0'
#Save solvated structure
print >> lp, 'savepdb mol %s_solv.pdb' %gname
print >> lp, 'saveamberparm mol %s_solv.prmtop %s_solv.inpcrd' \
%(gname, gname)
print >> lp, 'quit'
print >> lp, ' '
lp.close()
print 'Finish generating the leap input file.'
def gene_leaprc(gname, orpdbf, fipdbf, stpdbf, stfpf, ionids,\
ionmol2fs, ioninf, mcresname, naamol2fs, ff_choice, frcmodfs,
finfcdf, ileapf, model, watermodel='tip3p', paraset='cm'):
print "******************************************************************"
print "* *"
print "*=================Generating input file for leap=================*"
print "* *"
print "******************************************************************"
#---------------------Generate the new pdb file--------------------------
#mol0 is the old mol while mol is new mol file with new names
mol0, atids0, resids0 = get_atominfo_fpdb(orpdbf)
reslist0 = get_reslist(mol0, resids0)
mol, atids, resids = get_atominfo_fpdb(orpdbf)
#rename the residue names into AMBER style, e.g. HIS --> HID, HIP, HIE
mol = rename_res(mol, atids)
#get the disulfur bond information
disul = get_diS_bond(mol, atids)
#resname the old residue names to new ones if it is not metal ion
if model in [1, 2]:
metcenres1 = [] #Old residue ids
fp = open(stfpf, 'r')
for line in fp:
if line[0:4] != "LINK":
line = line.split('-')
if int(line[0]) not in metcenres1:
metcenres1.append(int(line[0]))
fp.close()
metcenres2 = mcresname #New residue names
resndict = {}
resns = []
for i in range(0, len(metcenres1)):
resndict[metcenres1[i]] = metcenres2[i]
resns.append(metcenres2[i])
for i in resndict.keys():
mol.residues[i].resname = resndict[i]
writepdb(mol, atids, fipdbf)
#----------------------------get the atom names which changed atom type
if model in [1, 2]:
atomdefs = {}
fp0 = open(stfpf, 'r')
for line in fp0:
if line[0:4] != "LINK":
line = line.strip('\n')
line = line.split()
if line[2] != line[4]:
atnewtype = line[4]
element = mol.atoms[int(line[1])].element
if atnewtype not in atomdefs.keys():
atomdefs[atnewtype] = element
else:
if element != atomdefs[atnewtype]:
raise pymsmtError(
'There are atoms in fingerprint file '
'of standard model with same atom type '
'but different element.')
fp0.close()
#---------------------Get the bond information, mol2 is the standard model
if model == 1:
mol2, atids2, resids2 = get_atominfo_fpdb(stpdbf)
blist = get_mc_blist(mol2, atids2, ionids, stfpf)
blist1 = [(i[0], i[1]) for i in blist]
#----------------------Generate the lib file and get the frcmod file name
if model == 2:
frcmodfs = []
for ionmol2f in ionmol2fs:
ionmol, ionatids, ionresids = get_atominfo(ionmol2f)
for i in ionatids:
element = ionmol.atoms[i].element
chg = int(ionmol.atoms[i].charge)
frcmodf = get_frcmod_fname(element, chg, watermodel, paraset)
if frcmodf not in frcmodfs:
frcmodfs.append(frcmodf)
elif model == 3 and ioninf != []:
#get the metal information
metresns = ioninf[0::4]
metatns = ioninf[1::4]
metelmts = ioninf[2::4]
metelmts = [i[0] + i[1:].lower() for i in metelmts]
metchgs = ioninf[3::4]
metchgs = [int(i) for i in metchgs]
#check the charge of the metal ions
for metchg in metchgs:
if metchg < -1 or metchg > 4:
raise pymsmtError(
'Could not deal with atomic ion which has charge '
'less than -1 or bigger than +4.')
frcmodfs = []
for i in range(0, len(metresns)):
if metchgs[
i] > 1: #if it is -1 or +1 ions, no need to create the lib file
gene_ion_libfile(metresns[i], metatns[i], metelmts[i],
metchgs[i])
frcmodf = get_frcmod_fname(metelmts[i], metchgs[i], watermodel,
paraset)
if frcmodf not in frcmodfs:
frcmodfs.append(frcmodf)
#-----------------------Generate the leap input file-----------------------
print 'Generating the leap input file...'
##Generate the tleap.in file
lp = open(ileapf, 'w')
if ff_choice in ['ff94', 'ff99', 'ff99SB', 'ff03', 'ff10']:
print >> lp, 'source oldff/leaprc.%s' % ff_choice
elif ff_choice in ['ff03.r1', 'ff12SB', 'ff14SB']:
print >> lp, 'source leaprc.%s' % ff_choice
print >> lp, 'source leaprc.gaff'
#Add atom types, for bonded model
if model in [1, 2]:
if atomdefs.keys() != []:
print >> lp, 'addAtomTypes {'
for i in atomdefs.keys():
print >> lp, ' { "%s" "%s" "sp3" }' % (i, atomdefs[i])
print >> lp, '}'
#load lib and frcmod files for monovalent ions (for salt)
if ff_choice in ['ff94', 'ff99', 'ff99SB', 'ff03', 'ff03.r1']:
print >> lp, 'loadoff atomic_ions.lib'
print >> lp, 'loadamberparams frcmod.ions1lsm_hfe_%s' % watermodel
#Load mol2 file for the refitting charge residues
if model in [1, 2]:
for i in resns:
print >> lp, '%s = loadmol2 %s.mol2' % (i, i)
elif model == 3:
for i in naamol2fs:
print >> lp, '%s = loadmol2 %s.mol2' % (i, i)
#Load frcmod files for non-standard residues and metal site
for i in frcmodfs:
print >> lp, 'loadamberparams %s' % i
if model == 1:
print >> lp, 'loadamberparams %s' % finfcdf
elif model == 2:
for frcmodf in frcmodfs:
print >> lp, 'loadamberparams %s' % frcmodf
elif model == 3:
for metresn in metresns:
print >> lp, 'loadoff %s.lib' % metresn
for frcmodf in frcmodfs:
print >> lp, 'loadamberparams %s' % frcmodf
#load pdb file
print >> lp, 'mol = loadpdb %s' % fipdbf
##The Disulfur Bond information
if disul != []:
for i in disul:
at1 = i[0]
at2 = i[1]
resid1 = mol.atoms[at1].resid
resid2 = mol.atoms[at2].resid
atname1 = mol.atoms[at1].atname
atname2 = mol.atoms[at2].atname
print >> lp, 'bond', 'mol.' + str(resid1) + '.' + atname1, 'mol.' + \
str(resid2) + '.' + atname2
##Bond including the metal ions
if model == 1:
for bond in blist1:
if list(set(bond) & set(ionids)) != []:
at1 = bond[0]
at2 = bond[1]
resid1 = mol.atoms[at1].resid
resid2 = mol.atoms[at2].resid
atname1 = mol.atoms[at1].atname
atname2 = mol.atoms[at2].atname
print >> lp, 'bond', 'mol.' + str(resid1) + '.' + atname1, 'mol.' + \
str(resid2) + '.' + atname2
##Nonstandard residues with nearby residues
if model in [1, 2]:
bondcmds = []
for i in metcenres1:
resname = mol0.residues[i].resname
print 'Renamed residues includes: ' + str(i) + '-' + resname
if i in reslist0.nterm:
cmdi = 'bond mol.' + str(i) + '.C' + ' mol.' + str(i +
i) + '.N'
if cmdi not in bondcmds:
bondcmds.append(cmdi)
elif i in reslist0.cterm:
cmdi = 'bond mol.' + str(i -
1) + '.C' + ' mol.' + str(i) + '.N'
if cmdi not in bondcmds:
bondcmds.append(cmdi)
elif i in reslist0.std:
cmdi = 'bond mol.' + str(i -
1) + '.C' + ' mol.' + str(i) + '.N'
if cmdi not in bondcmds:
bondcmds.append(cmdi)
cmdi = 'bond mol.' + str(i) + '.C' + ' mol.' + str(i +
1) + '.N'
if cmdi not in bondcmds:
bondcmds.append(cmdi)
for j in bondcmds:
print >> lp, j
#Save dry structure
print >> lp, 'savepdb mol %s_dry.pdb' % gname
print >> lp, 'saveamberparm mol %s_dry.prmtop %s_dry.inpcrd' \
%(gname, gname)
#Solvatebox
if watermodel == 'tip3p':
print >> lp, 'solvatebox mol TIP3PBOX 10.0'
elif watermodel == 'spce':
print >> lp, 'solvatebox mol SPCBOX 10.0'
print >> lp, 'loadamberparams frcmod.spce'
elif watermodel == 'tip4pew':
print >> lp, 'solvatebox mol TIP4PEWBOX 10.0'
print >> lp, 'loadamberparams frcmod.tip4pew'
#Add counter ions
print >> lp, 'addions mol Na+ 0'
print >> lp, 'addions mol Cl- 0'
#Save solvated structure
print >> lp, 'savepdb mol %s_solv.pdb' % gname
print >> lp, 'saveamberparm mol %s_solv.prmtop %s_solv.inpcrd' \
%(gname, gname)
print >> lp, 'quit'
print >> lp, ' '
lp.close()
print 'Finish generating the leap input file.'
