def callgmx(command, stdin=None, print_to_screen=False, print_command=True, **kwargs):
# Remove backup files.
rm_gmx_baks(os.getcwd())
# Call a GROMACS program as you would from the command line.
if GMXVERSION == 5:
csplit = ("gmx " + command.replace("gmx", "")).split()
else:
if command.split()[0] in gmxprogs:
csplit = ("g_%s" % command).split()
else:
csplit = command.split()
prog = os.path.join(gmxpath, csplit[0])
csplit[0] = prog + gmxsuffix
return _exec(" ".join(csplit), stdin=stdin, print_to_screen=print_to_screen, print_command=print_command, **kwargs)
def callgmx(command, stdin=None, print_to_screen=False, print_command=False, **kwargs):
# Remove backup files.
rm_gmx_baks(os.getcwd())
# Call a GROMACS program as you would from the command line.
if GMXVERSION == 5:
csplit = ('gmx ' + command.replace('gmx', '')).split()
else:
if command.split()[0] in gmxprogs:
csplit = ('g_%s' % command).split()
else:
csplit = command.split()
prog = os.path.join(gmxpath, csplit[0])
csplit[0] = prog + gmxsuffix
return _exec(' '.join(csplit), stdin=stdin, print_to_screen=print_to_screen, print_command=print_command, **kwargs)
def Calculate_AMBER(Structure, mdp_opts):
pbc = mdp_opts["pbc"].lower() == "xyz"
# Create AMBER inpcrd file
inpcrd = amber.AmberAsciiRestart("inpcrd", mode="w")
inpcrd.coordinates = np.array(Structure.positions.value_in_unit(
u.angstrom)).reshape(-1, 3)
inpcrd.box = Structure.box
inpcrd.close()
# sander insists on providing a trajectory to iterate over,
# so we feed it the same coordinates again. But we don't use it
# because the positions are imprecise.
mdcrd = amber.AmberMdcrd("mdcrd",
natom=len(Structure.atoms),
hasbox=pbc,
mode="w")
mdcrd.add_coordinates(
np.array(Structure.positions.value_in_unit(u.angstrom)).reshape(-1, 3))
if pbc:
mdcrd.add_box(Structure.box[:3])
mdcrd.close()
# Create AMBER prmtop object from ParmEd Structure :)
prmtop = amber.AmberParm.from_structure(Structure)
prmtop.write_parm("prmtop")
# Create AMBER mdin file and append some stuff
mdin = Mdin()
# Single point energies?
mdin.change('cntrl', 'imin', '5')
# Periodic boundary conditions?
if pbc:
mdin.change('cntrl', 'ntb', '1')
else:
mdin.change('cntrl', 'ntb', '0')
# Cutoff zero is really infinite
if float(mdp_opts['rlist']) == 0.0:
mdin.change('cntrl', 'cut', '9999')
else:
mdin.change('cntrl', 'cut', str(int(float(mdp_opts['rlist']) * 10)))
# Take zero MD steps
mdin.change('cntrl', 'nstlim', '0')
# Don't update nonbond parameters
mdin.change('cntrl', 'nsnb', '0')
# if mdp_opts['coulombtype'].lower() == 'pme':
# mdin.change('ewald','order',5)
# mdin.change('ewald','skinnb',0)
mdin.write("mdin")
# Nonbonded method
if mdp_opts['coulombtype'].lower() == 'pme':
with open("mdin", 'a') as f:
print >> f, """&ewald
order=5, skinnb=0
/"""
with open("mdin", 'a') as f:
print >> f, """&debugf
do_debugf=1, dumpfrc=1
/"""
# Call sander for energy and force
os.system('rm -f forcedump.dat')
_exec("sander -O -y mdcrd", print_command=False)
# Parse energy and force
ParseMode = 0
Energies = []
Forces = []
Force = []
iatom = 0
isAtom = [atom.atomic_number > 0 for atom in Structure.atoms]
for line in open('forcedump.dat'):
line = line.strip()
sline = line.split()
if ParseMode == 1:
if len(sline) == 1 and isfloat(sline[0]):
Energies.append(float(sline[0]) * 4.184)
ParseMode = 0
if ParseMode == 2:
if len(sline) == 3 and all(isfloat(sline[i]) for i in range(3)):
if isAtom[iatom]:
Force += [float(sline[i]) * 4.184 * 10 for i in range(3)]
iatom += 1
if len(Force) == 3 * sum(isAtom):
Forces.append(np.array(Force))
Force = []
ParseMode = 0
iatom = 0
if line == '0 START of Energies':
ParseMode = 1
elif line == '1 Total Force' or line == '2 Total Force':
ParseMode = 2
# Obtain energy components
ParseMode = 0
Ecomps = OrderedDict()
for line in open("mdout").readlines():
if "NSTEP = " in line:
ParseMode = 1
if ParseMode == 1:
if "=" not in line:
ParseMode = 0
continue
else:
ieq = None
wkey = []
# Assume the line is split-able
for i, w in enumerate(line.split()):
if w == '=':
ieq = i
elif i - 1 == ieq:
Ecomps.setdefault(' '.join(wkey),
[]).append(float(w) * 4.184)
wkey = []
else:
wkey.append(w)
Ecomps_Sav = OrderedDict()
for key in Ecomps:
if set(Ecomps[key]) == set([0.0]): continue
elif key.lower() in ['eptot', 'etot', 'volume', 'density']: continue
else:
Ecomps_Sav[key] = Ecomps[key][0]
Ecomps_Sav['EPTOT'] = Ecomps['EPtot'][0]
# Save just the first frame from the .mdcrd
Energies = Energies[0]
Forces = Forces[0]
return Energies, Forces, Ecomps_Sav
gmx_pdb.atomname[anum] = amb_gmx_amap[k][aname]
anameInResidue = []
anumInResidue = []
# Write the Gromacs-compatible PDB file
gmx_pdbfnm = os.path.splitext(sys.argv[1])[0] + "-gmx.pdb"
gmx_pdb.write(gmx_pdbfnm)
gmx_ffnames = {
'fb15': 'amberfb15',
'fb15ni': 'amberfb15ni',
'ildn': 'amber99sb-ildn'
}
amber_ffnames = {'fb15': 'fb15', 'fb15ni': 'fb15ni', 'ildn': 'ff99SBildn'}
# Set up the system in Gromacs
_exec("pdb2gmx -ff %s -f %s" % (gmx_ffnames[args.ff], gmx_pdbfnm), stdin="1\n")
# Set up the system in AMBER
amb_outpdbfnm = os.path.splitext(sys.argv[1])[0] + "-amb.pdb"
with open("stage.leap", 'w') as f:
print >> f, """source leaprc.{choice}
pdb = loadpdb {pdbin}
savepdb pdb {pdbout}
saveamberparm pdb prmtop inpcrd
quit
""".format(choice=amber_ffnames[args.ff],
pdbin=sys.argv[1],
pdbout=amb_outpdbfnm)
_exec("tleap -f stage.leap")
break
if mapped:
for anum, aname in zip(anumInResidue, anameInResidue):
gmx_pdb.atomname[anum] = amb_gmx_amap[k][aname]
anirs.append(anameInResidue)
anameInResidue = []
anumInResidue = []
# Write the Gromacs-compatible PDB file
gmx_pdbfnm = os.path.splitext(sys.argv[1])[0]+"-gmx.pdb"
gmx_pdb.write(gmx_pdbfnm)
gmx_ffnames = {'fb15':'amberfb15', 'fb15ni':'amberfb15ni', 'ildn':'amber99sb-ildn'}
amber_ffnames = {'fb15' : 'fb15', 'fb15ni':'fb15ni', 'ildn':'ff99SBildn'}
# Set up the system in Gromacs
_exec("pdb2gmx -ff %s -f %s" % (gmx_ffnames[args.ff], gmx_pdbfnm), stdin="1\n")
# Set up the system in AMBER
amb_outpdbfnm = os.path.splitext(sys.argv[1])[0]+"-amb.pdb"
with open("stage.leap", 'w') as f:
print >> f, """source leaprc.{choice}
pdb = loadpdb {pdbin}
savepdb pdb {pdbout}
saveamberparm pdb prmtop inpcrd
quit
""".format(choice = amber_ffnames[args.ff],
pdbin = sys.argv[1], pdbout = amb_outpdbfnm)
_exec("tleap -f stage.leap")
# raise RuntimeError
if gmx_acharge != chrm_acharge:
print "Atomic charges don't match for", resname, gmx_atom, chrm_atom
# raise RuntimeError
# Print the atoms that are renamed
# if gmx_aname != chrm_aname:
# print "%s (AMBER) %s <-> %s (CHARMM)" % (resname, chrm_aname, gmx_aname)
gmx_chrm_amap.setdefault(resname, OrderedDict())[gmx_aname] = chrm_aname
chrm_gmx_amap.setdefault(resname, OrderedDict())[chrm_aname] = gmx_aname
chrm_atomnames = OrderedDict([(k, set(v.keys())) for k, v in chrm_gmx_amap.items()])
max_reslen = max([len(v) for v in chrm_atomnames.values()])
pdb_in = sys.argv[1]
# rewrite the gmx pdb using mdtraj
_exec('python ~/scripts/manip_proteins/mdt_rewrite_pdb.py --p0 %s --pf mdt_%s' % (pdb_in, pdb_in))
# run pdb thru/chrm charmming
_exec('python ~/local/charmming/parser_v3.py mdt_%s' % (pdb_in))
# Begin with an GMX-compatible PDB file
# Please ensure by hand :)
pdb = Molecule(pdb_in, build_topology=False)
gmx_pdb = copy.deepcopy(pdb)
del gmx_pdb.Data['elem']
# Convert to a GROMACS-compatible PDB file
# This mainly involves renaming atoms and residues,
# notably hydrogen names.
# List of atoms in the current residue
def Calculate_AMBER(Structure, mdp_opts):
pbc = mdp_opts["pbc"].lower() == "xyz"
# Create AMBER inpcrd file
inpcrd = amber.AmberAsciiRestart("inpcrd", mode="w")
inpcrd.coordinates = np.array(Structure.positions.value_in_unit(u.angstrom)).reshape(-1, 3)
inpcrd.box = Structure.box
inpcrd.close()
# sander insists on providing a trajectory to iterate over,
# so we feed it the same coordinates again. But we don't use it
# because the positions are imprecise.
mdcrd = amber.AmberMdcrd("mdcrd", natom=len(Structure.atoms), hasbox=pbc, mode="w")
mdcrd.add_coordinates(np.array(Structure.positions.value_in_unit(u.angstrom)).reshape(-1, 3))
if pbc:
mdcrd.add_box(Structure.box[:3])
mdcrd.close()
# Create AMBER prmtop object from ParmEd Structure :)
prmtop = amber.AmberParm.from_structure(Structure)
prmtop.write_parm("prmtop")
# Create AMBER mdin file and append some stuff
mdin = Mdin()
# Single point energies?
mdin.change("cntrl", "imin", "5")
# Periodic boundary conditions?
if pbc:
mdin.change("cntrl", "ntb", "1")
else:
mdin.change("cntrl", "ntb", "0")
# Cutoff zero is really infinite
if float(mdp_opts["rlist"]) == 0.0:
mdin.change("cntrl", "cut", "9999")
else:
mdin.change("cntrl", "cut", str(int(float(mdp_opts["rlist"]) * 10)))
# Take zero MD steps
mdin.change("cntrl", "nstlim", "0")
# Don't update nonbond parameters
mdin.change("cntrl", "nsnb", "0")
# if mdp_opts['coulombtype'].lower() == 'pme':
# mdin.change('ewald','order',5)
# mdin.change('ewald','skinnb',0)
mdin.write("mdin")
# Nonbonded method
if mdp_opts["coulombtype"].lower() == "pme":
with open("mdin", "a") as f:
print >> f, """&ewald
order=5, skinnb=0
/"""
with open("mdin", "a") as f:
print >> f, """&debugf
do_debugf=1, dumpfrc=1
/"""
# Call sander for energy and force
os.system("rm -f forcedump.dat")
_exec("sander -O -y mdcrd", print_command=False)
# Parse energy and force
ParseMode = 0
Energies = []
Forces = []
Force = []
iatom = 0
isAtom = [atom.atomic_number > 0 for atom in Structure.atoms]
for line in open("forcedump.dat"):
line = line.strip()
sline = line.split()
if ParseMode == 1:
if len(sline) == 1 and isfloat(sline[0]):
Energies.append(float(sline[0]) * 4.184)
ParseMode = 0
if ParseMode == 2:
if len(sline) == 3 and all(isfloat(sline[i]) for i in range(3)):
if isAtom[iatom]:
Force += [float(sline[i]) * 4.184 * 10 for i in range(3)]
iatom += 1
if len(Force) == 3 * sum(isAtom):
Forces.append(np.array(Force))
Force = []
ParseMode = 0
iatom = 0
if line == "0 START of Energies":
ParseMode = 1
elif line == "1 Total Force" or line == "2 Total Force":
ParseMode = 2
# Obtain energy components
ParseMode = 0
Ecomps = OrderedDict()
for line in open("mdout").readlines():
if "NSTEP = " in line:
ParseMode = 1
if ParseMode == 1:
if "=" not in line:
ParseMode = 0
continue
else:
ieq = None
wkey = []
# Assume the line is split-able
for i, w in enumerate(line.split()):
if w == "=":
ieq = i
elif i - 1 == ieq:
Ecomps.setdefault(" ".join(wkey), []).append(float(w) * 4.184)
wkey = []
else:
wkey.append(w)
Ecomps_Sav = OrderedDict()
for key in Ecomps:
if set(Ecomps[key]) == set([0.0]):
continue
elif key.lower() in ["eptot", "etot", "volume", "density"]:
continue
else:
Ecomps_Sav[key] = Ecomps[key][0]
Ecomps_Sav["EPTOT"] = Ecomps["EPtot"][0]
# Save just the first frame from the .mdcrd
Energies = Energies[0]
Forces = Forces[0]
return Energies, Forces, Ecomps_Sav
