def protonate(inpdbfile, outpdbfile, pH):
"""Generate a protonated PDB file from a template PDB using MCCE."""
thisdir = os.path.abspath(os.curdir)
mcceOut = os.path.abspath(outpdbfile)
prmFile = '../mccetools/prmfiles/run.prm.quick'
prmFile = os.path.abspath(prmFile)
mcce.protonatePDB(inpdbfile, mcceOut, pH, os.environ['MCCE_LOCATION'], cleanup=True, prmfile=prmFile, labeledPDBOnly=False)
os.chdir(thisdir)
def shoveItThrough(protein):
# determine base name
print "PDB File: " + protein.pdbfile
print "Sequence File: " + protein.seqfile
extInd = protein.seqfile.rindex(".")
baseName = protein.seqfile[0:extInd]
# run modelPDB
if (1):
modelPDBOut = baseName + "_modelPDB_out.pdb"
myModel = modelPDB.ModelPDB()
myModel.makeModel(protein.pdbfile, protein.seqfile, modelPDBOut)
# run mcce
if (1):
mcceOut = baseName + "_mcce_out.pdb"
mcceOut = os.path.abspath(mcceOut)
prmFile = '../../mccetools/prmfiles/run.prm.quick'
prmFile = os.path.abspath(prmFile)
params = mcce.read_paramfile(prmFile)
mcce.print_prm(params)
mcce.protonatePDB(modelPDBOut,
mcceOut,
protein.pH,
os.environ['MCCE_LOCATION'],
cleanup=True,
prmfile=prmFile)
# run gromacs setup
if (1):
gromacsOut = baseName + "_final.pdb"
forcefield = 'ffamber99p'
# g = system.GromacsSystem(mcceOut, useff=forcefield) # the old gromacstools way
g = System(mcceOut, useff=forcefield)
g.setup.setSaltConditions(protein.salt, protein.saltconc)
g.setup.set_boxSoluteDistance(
0.9
) # <--- ***Greg!!!*** <--- periodic box margin distance, in nanometers
thisOutDir = os.path.join(thisdir, baseName)
print 'Writing equilibration directory to', thisOutDir, '...'
if os.path.exists(thisOutDir) == False:
os.mkdir(thisOutDir)
g.prepare(outname=gromacsOut,
outdir=thisOutDir,
verbose=True,
cleanup=False,
debug=DEBUG,
protocol='racecar2',
checkForFatalErrors=True)
# cleanup
if not DEBUG:
os.remove(modelPDBOut)
os.remove(mcceOut)
def shoveItThrough(protein):
# determine base name
print "PDB File: " + protein.pdbfile
print "Sequence File: " + protein.seqfile
extInd = protein.seqfile.rindex(".")
baseName = protein.seqfile[0:extInd]
# run modelPDB
if 1:
modelPDBOut = baseName + "_modelPDB_out.pdb"
myModel = modelPDB.ModelPDB()
myModel.makeModel(protein.pdbfile, protein.seqfile, modelPDBOut)
# run mcce
if 1:
mcceOut = baseName + "_mcce_out.pdb"
mcceOut = os.path.abspath(mcceOut)
prmFile = "../../mccetools/prmfiles/run.prm.quick"
prmFile = os.path.abspath(prmFile)
params = mcce.read_paramfile(prmFile)
mcce.print_prm(params)
mcce.protonatePDB(modelPDBOut, mcceOut, protein.pH, os.environ["MCCE_LOCATION"], cleanup=True, prmfile=prmFile)
# run gromacs setup
if 1:
gromacsOut = baseName + "_final.pdb"
forcefield = "ffamber99p"
# g = system.GromacsSystem(mcceOut, useff=forcefield) # the old gromacstools way
g = System(mcceOut, useff=forcefield)
g.setup.setSaltConditions(protein.salt, protein.saltconc)
g.setup.set_boxSoluteDistance(0.9) # <--- ***Greg!!!*** <--- periodic box margin distance, in nanometers
thisOutDir = os.path.join(thisdir, baseName)
print "Writing equilibration directory to", thisOutDir, "..."
if os.path.exists(thisOutDir) == False:
os.mkdir(thisOutDir)
g.prepare(
outname=gromacsOut,
outdir=thisOutDir,
verbose=True,
cleanup=False,
debug=DEBUG,
protocol="racecar2",
checkForFatalErrors=True,
)
# cleanup
if not DEBUG:
os.remove(modelPDBOut)
os.remove(mcceOut)
def protonate(inpdbfile, outpdbfile, pH):
"""Generate a protonated PDB file from a template PDB using MCCE."""
thisdir = os.path.abspath(os.curdir)
mcceOut = os.path.abspath(outpdbfile)
prmFile = '../mccetools/prmfiles/run.prm.quick'
prmFile = os.path.abspath(prmFile)
mcce.protonatePDB(inpdbfile,
mcceOut,
pH,
os.environ['MCCE_LOCATION'],
cleanup=True,
prmfile=prmFile,
labeledPDBOnly=False)
os.chdir(thisdir)
def shoveit(protein,
outdir,
forcefield='ffamber99p',
protocol='racecar2',
captermini=False,
debug=False,
verbose=True,
cleanup=False,
implicitOptions=None,
useTable=None,
MultiChain=False,
SkipMCCE=False):
"""Shoves a pipelineProtein object through the entire MODELLER -> MCCE --> gromacs pipeline.
For capping the termini with ACE and NH2:
The Modeller program has a nice way of doing
residue 'patches', so this will be used for adding the caps. The program will do the following:
1. Thread the sequence via Modeller, which will patch the termini caps--> PDB
2. Calculate the protonation state via MCCE (which will know how to handle ACE and NH2 residues because
of the patches ace.tpl and nh2.tpl in param04 and param08 --> PDB with ffamber-named residues
3. feed through gromacstools in normal fashion
OPTIONS
MultiChain If set to True, will thread a multichain model. NOTE: the sequence of the
mutiple chains (in the protein object) must be demarcated by '/'. Example:
AKEEFWVY/AWEKKLELEQVID
"""
thisdir = '%s' % os.path.abspath(os.curdir)
protein.setup(
outdir
) # Set up modelPDBout filenames and such using the basename of the outdir
protein.print_info()
# Build a PDB model from the pdbTemplate using MODELLER
if MultiChain:
thread_model(protein.pdbfile,
protein.seqfile,
protein.modelPDBout,
captermini=captermini)
else:
thread_model(protein.pdbfile,
protein.seqfile,
protein.modelPDBout,
captermini=captermini)
# run mcce
mcceOut = os.path.abspath(protein.mccePDBout)
if SkipMCCE:
# reformat the MODELLER PDB with the right names
fin = open(protein.modelPDBout, 'r')
modelPDBlines = fin.readlines()
fin.close()
npdb = mcce.rename.nest_pdb(modelPDBlines)
outlines = mcce.rename.unnest_pdb(
mcce.rename.rename_MODELLER_termini(npdb))
fout = open(mcceOut, 'w')
fout.writelines(outlines)
fout.close()
print 'Writing PDB to', mcceOut
else:
prmFile = '../../mccetools/prmfiles/run.prm.quick'
prmFile = os.path.abspath(prmFile)
if (captermini):
mcce.protonatePDB(protein.modelPDBout,
mcceOut,
protein.pH,
os.environ['MCCE_LOCATION'],
cleanup=cleanup,
prmfile=prmFile,
renameTermini=False)
else:
mcce.protonatePDB(protein.modelPDBout,
mcceOut,
protein.pH,
os.environ['MCCE_LOCATION'],
cleanup=cleanup,
prmfile=prmFile)
# run gromacs setup
if (1):
gromacsOut = protein.basename + "_final.pdb"
# g = system.GromacsSystem(mcceOut, useff=forcefield) # the old gromacstools way
g = System(mcceOut,
finalOutputDir=outdir,
finalOutputName=protein.basename,
useff=forcefield)
g.setup.setSaltConditions(protein.salt, protein.saltconc)
if protein.cosolvent != None:
g.setup.setCosolventConditions(protein.cosolvent,
protein.cosolventconc)
if protein.boxProtocol == 'small':
g.setup.set_boxType = 'octahedron'
g.setup.set_boxSoluteDistance(
1.5) # periodic box margin distance, in nanometers
elif protein.boxProtocol == 'big':
g.setup.set_boxType = 'octahedron'
g.setup.setUseAbsBoxSize(True)
g.setup.setAbsBoxSize(
'7.0') # periodic box absolute size, in nanometers (string)
elif protein.boxProtocol[0:3] == 'unf':
g.setup.set_boxType = 'octahedron'
g.setup.setUseAbsBoxSize(True)
if protein.boxProtocol == 'unf100':
g.setup.setAbsBoxSize('10.0')
if protein.boxProtocol == 'unf110':
g.setup.setAbsBoxSize('11.0')
if protein.boxProtocol == 'unf120':
g.setup.setAbsBoxSize('12.0')
thisOutDir = os.path.join(thisdir, protein.basename)
print 'Writing equilibration directory to', thisOutDir, '...'
if os.path.exists(thisOutDir) == False:
os.mkdir(thisOutDir)
os.chdir(thisOutDir)
g.prepare(verbose=verbose,
cleanup=cleanup,
debug=debug,
protocol=protocol,
checkForFatalErrors=True,
implicitOptions=implicitOptions,
useTable=useTable)
if (1):
# cleanup
if not DEBUG:
if os.path.exists(protein.modelPDBout):
os.remove(protein.modelPDBout)
if os.path.exists(protein.mccePDBout):
os.remove(protein.mccePDBout)
os.chdir(thisdir)
def shoveit(protein, outdir, forcefield='ffamber99p', protocol='racecar2', captermini=False, debug=False, verbose=True, cleanup=False, implicitOptions=None, useTable=None, MultiChain=False, SkipMCCE=False):
"""Shoves a pipelineProtein object through the entire MODELLER -> MCCE --> gromacs pipeline.
For capping the termini with ACE and NH2:
The Modeller program has a nice way of doing
residue 'patches', so this will be used for adding the caps. The program will do the following:
1. Thread the sequence via Modeller, which will patch the termini caps--> PDB
2. Calculate the protonation state via MCCE (which will know how to handle ACE and NH2 residues because
of the patches ace.tpl and nh2.tpl in param04 and param08 --> PDB with ffamber-named residues
3. feed through gromacstools in normal fashion
OPTIONS
MultiChain If set to True, will thread a multichain model. NOTE: the sequence of the
mutiple chains (in the protein object) must be demarcated by '/'. Example:
AKEEFWVY/AWEKKLELEQVID
"""
thisdir = '%s'%os.path.abspath(os.curdir)
protein.setup(outdir) # Set up modelPDBout filenames and such using the basename of the outdir
protein.print_info()
# Build a PDB model from the pdbTemplate using MODELLER
if MultiChain:
thread_model(protein.pdbfile, protein.seqfile, protein.modelPDBout, captermini=captermini)
else:
thread_model(protein.pdbfile, protein.seqfile, protein.modelPDBout, captermini=captermini)
# run mcce
mcceOut = os.path.abspath(protein.mccePDBout)
if SkipMCCE:
# reformat the MODELLER PDB with the right names
fin = open(protein.modelPDBout,'r')
modelPDBlines = fin.readlines()
fin.close()
npdb = mcce.rename.nest_pdb(modelPDBlines)
outlines = mcce.rename.unnest_pdb(mcce.rename.rename_MODELLER_termini(npdb))
fout = open(mcceOut,'w')
fout.writelines(outlines)
fout.close()
print 'Writing PDB to', mcceOut
else:
prmFile = '../../mccetools/prmfiles/run.prm.quick'
prmFile = os.path.abspath(prmFile)
if (captermini):
mcce.protonatePDB(protein.modelPDBout, mcceOut, protein.pH, os.environ['MCCE_LOCATION'], cleanup=cleanup, prmfile=prmFile, renameTermini=False)
else:
mcce.protonatePDB(protein.modelPDBout, mcceOut, protein.pH, os.environ['MCCE_LOCATION'], cleanup=cleanup, prmfile=prmFile)
# run gromacs setup
if (1):
gromacsOut = protein.basename + "_final.pdb"
# g = system.GromacsSystem(mcceOut, useff=forcefield) # the old gromacstools way
g = System(mcceOut, finalOutputDir=outdir, finalOutputName=protein.basename, useff=forcefield)
g.setup.setSaltConditions(protein.salt, protein.saltconc)
if protein.cosolvent != None:
g.setup.setCosolventConditions(protein.cosolvent, protein.cosolventconc)
if protein.boxProtocol == 'small':
g.setup.set_boxType = 'octahedron'
g.setup.set_boxSoluteDistance(1.5) # periodic box margin distance, in nanometers
elif protein.boxProtocol == 'big':
g.setup.set_boxType = 'octahedron'
g.setup.setUseAbsBoxSize(True)
g.setup.setAbsBoxSize('7.0') # periodic box absolute size, in nanometers (string)
elif protein.boxProtocol[0:3] == 'unf':
g.setup.set_boxType = 'octahedron'
g.setup.setUseAbsBoxSize(True)
if protein.boxProtocol == 'unf100':
g.setup.setAbsBoxSize('10.0')
if protein.boxProtocol == 'unf110':
g.setup.setAbsBoxSize('11.0')
if protein.boxProtocol == 'unf120':
g.setup.setAbsBoxSize('12.0')
thisOutDir = os.path.join(thisdir, protein.basename)
print 'Writing equilibration directory to',thisOutDir,'...'
if os.path.exists(thisOutDir) == False:
os.mkdir(thisOutDir)
os.chdir(thisOutDir)
g.prepare(verbose=verbose, cleanup=cleanup, debug=debug, protocol=protocol, checkForFatalErrors=True, implicitOptions=implicitOptions, useTable=useTable)
if(1):
# cleanup
if not DEBUG:
if os.path.exists(protein.modelPDBout):
os.remove(protein.modelPDBout)
if os.path.exists(protein.mccePDBout):
os.remove(protein.mccePDBout)
os.chdir(thisdir)
#
# The parameters used in the MCCE run can be found in the prmfile specified below
#
# Vincent Voelz
# May 19 2007
#
import mmtools.mccetools.mcce as mcce
import os, sys
### INPUT LINES ####
#
# Specify the input and output PDB filenames
# NOTE: pdbfile and outpdbfile should be local (not absolute) paths for this project
pdbfile = '3gb1_testing.pdb'
outpdbfile = os.path.join(os.curdir,'3gb1_testing_protonated.pdb')
# Specify the pH
pH = 7.0
# Specify a MCCE parameter file with the desired set of parameters for calculating the pKa
prmfile = '../prmfiles/run.prm.quick'
prmfile = os.path.abspath(prmfile)
# Specify additional or different parameters than prmfile, if desired.
# xtraprms = {'TITR_PH0':'3.0'}
# Perform titration.
### work is done in a temporary dir; Setting cleanup=True will erase these temporary files
mcce.protonatePDB(pdbfile, outpdbfile, pH, os.environ['MCCE_LOCATION'], cleanup=False, prmfile=prmfile)
#
import mmtools.mccetools.mcce as mcce
import os, sys
### INPUT LINES ####
#
# Specify the input and output PDB filenames
# NOTE: pdbfile and outpdbfile should be local (not absolute) paths for this project
pdbfile = '3gb1_testing.pdb'
outpdbfile = os.path.join(os.curdir, '3gb1_testing_protonated.pdb')
# Specify the pH
pH = 7.0
# Specify a MCCE parameter file with the desired set of parameters for calculating the pKa
prmfile = '../prmfiles/run.prm.quick'
prmfile = os.path.abspath(prmfile)
# Specify additional or different parameters than prmfile, if desired.
# xtraprms = {'TITR_PH0':'3.0'}
# Perform titration.
### work is done in a temporary dir; Setting cleanup=True will erase these temporary files
mcce.protonatePDB(pdbfile,
outpdbfile,
pH,
os.environ['MCCE_LOCATION'],
cleanup=False,
prmfile=prmfile)
