def build_gmx(protein, outdir, forcefield='ffamber99p', protocol='racecar2'):
"""Builds a gromacs project according to the specs in the pipelineProtein object. Assumes
the protein.pdbfile is in the right (AMBER) format."""
if os.path.exists(outdir) == False:
os.mkdir(outdir)
baseName = protein.getBasename(protein.pdbfile)
gromacsOut = baseName + "_final"
g = System(protein.pdbfile,
finalOutputDir=outdir,
finalOutputName=gromacsOut,
useff=forcefield)
g.setup.setSaltConditions(protein.salt, protein.saltconc)
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(
'8.0') # periodic box absolute size, in nanometers (string)
g.prepare(outname=gromacsOut,
outdir=outdir,
verbose=True,
cleanup=False,
debug=DEBUG,
protocol='racecar2',
checkForFatalErrors=True)
def shoveItThrough(protein, forcefield):
thisdir = os.curdir
# determine base name
print "PDB File: " + protein.pdbfile
print "Sequence File: " + protein.seqfile
extInd = protein.seqfile.rindex(".")
baseName = protein.seqfile[0:extInd]
# run gromacs setup
if (1):
outname = baseName + "_final"
g = System(protein.pdbfile, useff=forcefield)
g.setup.setSaltConditions(protein.salt, protein.saltconc)
g.setup.set_boxSoluteDistance(
0.9
) # <--- ***Greg!!!*** <--- periodic box margin distance, in nanometers
outdir = os.path.abspath(os.path.join(thisdir, baseName))
print 'Writing equilibration directory to', outdir, '...'
if os.path.exists(outdir) == False:
os.mkdir(outdir)
g.prepare(outname=outname,
outdir=outdir,
verbose=True,
cleanup=False,
debug=DEBUG,
protocol='racecar2',
checkForFatalErrors=True)
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 build_gmx(protein, outdir, forcefield='ffamber99p', protocol='racecar2'):
"""Builds a gromacs project according to the specs in the pipelineProtein object. Assumes
the protein.pdbfile is in the right (AMBER) format."""
if os.path.exists(outdir) == False:
os.mkdir(outdir)
baseName = protein.getBasename( protein.pdbfile )
gromacsOut = baseName + "_final"
g = System(protein.pdbfile, finalOutputDir=outdir, finalOutputName=gromacsOut, useff=forcefield)
g.setup.setSaltConditions(protein.salt, protein.saltconc)
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('8.0') # periodic box absolute size, in nanometers (string)
g.prepare(outname=gromacsOut, outdir=outdir, verbose=True, cleanup=False, debug=DEBUG, protocol='racecar2', checkForFatalErrors=True)
def shoveItThrough(protein, forcefield):
thisdir = os.curdir
# determine base name
print "PDB File: " + protein.pdbfile
print "Sequence File: " + protein.seqfile
extInd = protein.seqfile.rindex(".")
baseName = protein.seqfile[0:extInd]
# run gromacs setup
if (1):
outname = baseName + "_final"
g = System(protein.pdbfile, useff=forcefield)
g.setup.setSaltConditions(protein.salt, protein.saltconc)
g.setup.set_boxSoluteDistance(0.9) # <--- ***Greg!!!*** <--- periodic box margin distance, in nanometers
outdir = os.path.abspath(os.path.join(thisdir, baseName))
print 'Writing equilibration directory to',outdir,'...'
if os.path.exists(outdir) == False:
os.mkdir(outdir)
g.prepare(outname=outname, outdir=outdir, verbose=True, cleanup=False, debug=DEBUG, protocol='racecar2', checkForFatalErrors=True)
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)
# copy the box dimensions from the template to the coil groStructure
g.boxstring = boxstr
# write the coil.gro (no solvent yet) to a tmpdir
tmpdir = tempfile.mkdtemp() # temporary directory for unfolded pdbs
coilgrofile = os.path.join(tmpdir,'coil')
print 'Writing', coilgrofile, '...'
g.write( coilgrofile ) # gromacstools.GromacsData forces us to save this using only the basename
coilgrofile = coilgrofile + '.gro' # correct to reflect the full name
# write a single molecule of water *.gro to the tmpdir
growater = os.path.join(tmpdir,'ffamber_tip3p_single.gro')
fout = open( growater, 'w')
fout.write("""TIP3P
3
1SOL OW 1 1.336 1.583 0.888 0.1910 -0.3183 -0.5328
1SOL HW1 2 1.399 1.553 0.953 -0.9817 -0.4598 0.5822
1SOL HW2 3 1.287 1.652 0.933 -2.0169 -1.8033 -0.5086
2.48706 2.48706 2.48706
""")
fout.close()
# prepare a resolvated grofile from the tempolate grofile -- this will correct the protonation state too
s = System(coilgrofile, finalOutputDir=outdir, finalOutputName=protein.basename, useff=forcefield) # a gromacstools.System.System() object
s.prepareResolvatedFromTemplate( coilgrofile, groTemplate, growater, protocol=protocol)
tmpdir = tempfile.mkdtemp() # temporary directory for unfolded pdbs
coilgrofile = os.path.join(tmpdir, 'coil')
print 'Writing', coilgrofile, '...'
g.write(
coilgrofile
) # gromacstools.GromacsData forces us to save this using only the basename
coilgrofile = coilgrofile + '.gro' # correct to reflect the full name
# write a single molecule of water *.gro to the tmpdir
growater = os.path.join(tmpdir, 'ffamber_tip3p_single.gro')
fout = open(growater, 'w')
fout.write("""TIP3P
3
1SOL OW 1 1.336 1.583 0.888 0.1910 -0.3183 -0.5328
1SOL HW1 2 1.399 1.553 0.953 -0.9817 -0.4598 0.5822
1SOL HW2 3 1.287 1.652 0.933 -2.0169 -1.8033 -0.5086
2.48706 2.48706 2.48706
""")
fout.close()
# prepare a resolvated grofile from the tempolate grofile -- this will correct the protonation state too
s = System(coilgrofile,
finalOutputDir=outdir,
finalOutputName=protein.basename,
useff=forcefield) # a gromacstools.System.System() object
s.prepareResolvatedFromTemplate(coilgrofile,
groTemplate,
growater,
protocol=protocol)
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 setup_binding_free_energy(protein_pdb_filename, ligand_filename, work_path, nreplicates_solvent = 1, nreplicates_complex = 1):
"""Set up generalized ensemble simulation to calculate a protein-ligand binding free energy.
ARGUMENTS
protein_pdb_filename (string) - filename of PDB file for the protein, without any missing heavy atoms and with appropriate protonation state already assigned
ligand_filename (string) - filename of some type OpenEye can read (e.g. mol2) describing the ligand with suitable docked coordinates
work_path (string) - directory to place files for binding free energy calculation (created if does not already exist)
OPTIONAL ARGUMENTS
nreplicates_solvent (int) - number of replicates to set up of solvated ligand (default: 1)
nreplicates_complex (int) - number of replicates to set up of the complexed ligand (default: 1)
"""
# parameters
forcefield = 'ffamber96' # forcefield
box_clearance_in_nm = 0.3 # clearance from system to box edges (in nm) # DEBUG set to 1.0
# gromacs filenames
pdb2gmx = 'pdb2gmx_d'
editconf = 'editconf_d'
genbox = 'genbox_d'
grompp = 'grompp_d'
mdrun = 'mdrun_d'
# Create directory for binding free energy calculation if it doesn't exist.
#DEBUG os.makedirs(work_path)
# SET UP PROTEIN TOPOLOGY
print "\nConstructing protein topology..."
# Create .top and .gro files for protein using pdb2gmx and desired forcefield
# look up forcefield index
lines = readFile(os.path.join(os.environ['GMXDATA'], 'top', 'FF.dat'))
for forcefield_index in range(1, len(lines)):
if lines[forcefield_index].find(forcefield) != -1: break
forcefield_index -= 1
# run pdb2gmx
protein_gro_filename = os.path.join(work_path, 'protein.gro')
protein_top_filename = os.path.join(work_path, 'protein.top')
command = 'echo %(forcefield_index)d | %(pdb2gmx)s -f %(protein_pdb_filename)s -o %(protein_gro_filename)s -p %(protein_top_filename)s -ignh -H14' % vars()
print command
#DEBUG output = commands.getoutput(command)
#DEBUG print output
# SET UP LIGAND TOPOLOGY
print "\nConstructing ligand topology..."
# Read the ligand into OEMol.
ligand = readMolecule(ligand_filename, normalize = True)
# Generate GAFF parameters for gromacs for small molecule, using antechamber to generate AM1-BCC charges.
ligand_top_filename = os.path.join(work_path,'ligand.top')
ligand_gro_filename = os.path.join(work_path,'ligand.gro')
#DEBUG parameterizeForGromacs(ligand, topology_filename = ligand_top_filename, coordinate_filename = ligand_gro_filename, charge_model = 'bcc', resname = 'LIG')
# Modify gromacs topology file for alchemical free energy calculation.
#DEBUG perturbGromacsTopology(os.path.join(work_path,'ligand.top'), ligand)
# SET UP SOLVATED LIGAND
print "\nSetting up solvated ligand..."
# Create directory to contain ligand in solution.
solvated_ligand_path = os.path.join(work_path, 'solvated-ligand')
#DEBUG os.makedirs(solvated_ligand_path)
# Convert gromacs topology to an .itp file suitable for inclusion.
top_to_itp(os.path.join(work_path,'ligand.top'), os.path.join(solvated_ligand_path,'solute.itp'), moleculetype = 'solute')
# write enlarged box for solvent
system_gro_filename = os.path.join(solvated_ligand_path, 'system.gro')
system_top_filename = os.path.join(solvated_ligand_path, 'system.top')
command = '%(editconf)s -f %(ligand_gro_filename)s -o %(system_gro_filename)s -bt octahedron -d %(box_clearance_in_nm)f' % vars()
print command
output = commands.getoutput(command)
print output
# write topology for system
contents = """
; amber forcefield
#include "ffamber03.itp"
; my molecule
#include "solute.itp"
; TIP3P water
#include "ffamber_tip3p.itp"
[ system ]
solute
[ molecules ]
; Compound nmols
solute 1
""" % vars()
writeFile(system_top_filename, contents)
# solvate
command = '%(genbox)s -cp %(system_gro_filename)s -cs ffamber_tip3p.gro -o %(system_gro_filename)s -p %(system_top_filename)s' % vars()
print command
output = commands.getoutput(command)
print output
# construct .mdp files
mdpfile = MdpFile(compose_blocks(['header', 'minimization', 'nonbonded-solvent', 'output']))
mdpfile.write(os.path.join(solvated_ligand_path, 'minimization-unconstrained.mdp'))
mdpfile = MdpFile(compose_blocks(['header', 'minimization', 'nonbonded-solvent', 'constraints', 'output']))
mdpfile.write(os.path.join(solvated_ligand_path, 'minimization-constrained.mdp'))
mdpfile = MdpFile(compose_blocks(['header', 'dynamics', 'nonbonded-solvent', 'constraints', 'thermostat', 'barostat', 'free-energy', 'output']))
mdpfile.randomizeSeed() # randomize velocities
mdpfile.write(os.path.join(solvated_ligand_path, 'production.mdp'))
# write run script
contents = """\
#/bin/tcsh
source /Users/jchodera/local/gromacs-3.1.4-fe/i386-apple-darwin8.11.1/bin/GMXRC.csh
# unconstrained minimization
%(grompp)s -f minimization-unconstrained.mdp -c system.gro -p system.top -o minimization-unconstrained.tpr -maxwarn 10000
%(mdrun)s -s minimization-unconstrained.tpr -x minimization-unconstrained.xtc -c minimized-unconstrained.gro -e minimization-unconstrained.edr -g minimization-unconstrained.log
# constrained minimization
%(grompp)s -f minimization-constrained.mdp -c minimized-unconstrained.gro -p system.top -o minimization-constrained.tpr -maxwarn 10000
%(mdrun)s -s minimization-constrained.tpr -x minimization-constrained.xtc -c minimized-constrained.gro -e minimization-constrained.edr -g minimization-constrained.log
# production
%(grompp)s -f production.mdp -c minimized-unconstrained.gro -p system.top -o production.tpr -maxwarn 10000
%(mdrun)s -s production.tpr -o production.trr -x production.xtc -c production.gro -e production.edr -g production.log
echo 0 | trjconv_d -f production.xtc -o production.pdb -s production.tpr
""" % vars()
writeFile(os.path.join(solvated_ligand_path, 'run.sh'), contents)
# SET UP SOLVATED COMPLEX
# Create directory to contain complex.
complex_path = os.path.join(work_path, 'solvated-complex')
#DEBUG os.makedirs(complex_path)
# Merge protein and liand .top files.
complex_top_filename = os.path.join(complex_path, 'complex.top')
complex_gro_filename = os.path.join(complex_path, 'complex.gro')
merge_protein_ligand_topologies(protein_top_filename, protein_gro_filename, ligand_top_filename, ligand_gro_filename, complex_top_filename, complex_gro_filename)
# Alter topology file to use ffamber TIP3P.
# system.useTIP3P(complex_top_filename)
# Determine total charge.
total_charge = totalCharge(complex_top_filename)
print "total_charge = %f" % total_charge
# Create a System object to help us out.
system = System(protein_pdb_filename, finalOutputDir = complex_path, finalOutputName = "protein", useff = forcefield)
system.setup.setSaltConditions('MgCl2', 0.010)
system.setup.set_boxType = 'octahedron'
system.setup.set_boxSoluteDistance(box_clearance_in_nm)
system.files.topfile = complex_top_filename
system.totalChargeBeforeIons = total_charge
# Create a periodic boundary conditions box.
command = '%(editconf)s -bt octahedron -f %(complex_gro_filename)s -o %(complex_gro_filename)s -d %(box_clearance_in_nm)f' % vars()
output = commands.getoutput(command)
print output
# solvate the box with TIP3P water
command = '%(genbox)s -cp %(complex_gro_filename)s -cs ffamber_tip3p.gro -o %(complex_gro_filename)s -p %(complex_top_filename)s' % vars()
output = commands.getoutput(command)
print output
# calculate how many ions to add to the box
[np, nn, nwaters] = system.counterions()
print "Adding %(np)d positive and %(nn)d negative to %(nwaters)d waters" % vars()
# minimize the system
### make a tpr file with grompp
#grompp = '%s/grompp -f %s -c %s -o %s -p %s '%(os.environ['GMXPATH'], self.files.mdpfile_Minimization, self.files.grofile, self.files.tprfile, self.files.topfile)
#self.rungmx( grompp, mockrun=self.mockrun, checkForFatalErrors=self.checkForFatalErrors )
### run minimization
#minimize = '%s/mdrun -v -s %s -c %s '%(os.environ['GMXPATH'], self.files.tprfile, self.files.next_gro() )
#self.rungmx( minimize, mockrun=self.mockrun, checkForFatalErrors=self.checkForFatalErrors )
#self.files.increment_gro() # must increment filename for any new gmx file
# do the rest of the preparation steps
#self.postSolvationPreparationSteps()
# construct .mdp files
mdpfile = MdpFile(compose_blocks(['header', 'minimization', 'nonbonded-solvent', 'output']))
mdpfile.write(os.path.join(complex_path, 'minimization-unconstrained.mdp'))
mdpfile = MdpFile(compose_blocks(['header', 'minimization', 'nonbonded-solvent', 'constraints', 'output']))
mdpfile.write(os.path.join(complex_path, 'minimization-constrained.mdp'))
mdpfile = MdpFile(compose_blocks(['header', 'dynamics', 'nonbonded-solvent', 'constraints', 'thermostat', 'barostat', 'free-energy', 'output']))
mdpfile.randomizeSeed() # randomize velocities
mdpfile.write(os.path.join(complex_path, 'production.mdp'))
# write run script for minimization and production
contents = """\
#/bin/tcsh
source /Users/jchodera/local/gromacs-3.1.4-fe/i386-apple-darwin8.11.1/bin/GMXRC.csh
# unconstrained minimization
%(grompp)s -f minimization-unconstrained.mdp -c system.gro -p system.top -o minimization-unconstrained.tpr -maxwarn 10000
%(mdrun)s -s minimization-unconstrained.tpr -x minimization-unconstrained.xtc -c minimized-unconstrained.gro -e minimization-unconstrained.edr -g minimization-unconstrained.log
# constrained minimization
%(grompp)s -f minimization-constrained.mdp -c minimized-unconstrained.gro -p system.top -o minimization-constrained.tpr -maxwarn 10000
%(mdrun)s -s minimization-constrained.tpr -x minimization-constrained.xtc -c minimized-constrained.gro -e minimization-constrained.edr -g minimization-constrained.log
# production
%(grompp)s -f production.mdp -c minimized-unconstrained.gro -p system.top -o production.tpr -maxwarn 10000
%(mdrun)s -s production.tpr -o production.trr -x production.xtc -c production.gro -e production.edr -g production.log
echo 0 | trjconv_d -f production.xtc -o production.pdb -s production.tpr
""" % vars()
writeFile(os.path.join(complex_path, 'run.sh'), contents)
# Convert gromacs topology to an .itp file suitable for inclusion.
# top_to_itp(os.path.join(molecule_path,'solute.top'), os.path.join(molecule_path,'solute.itp'), moleculetype = molecule_name)
return