with open(confFile,"w") as f:
f.write(proteinString)
# if args.mutatations:
# #TODO set correct filenames
# args = ['Scwrl4','-i',confFile,'-o','confs/test.pdb']
# md_tools.executeCommand(args)
# args = ['Scwrl4','-i','confs/test.pdb','-o',confFile,'-s',scrwl_sequence_file]
# md_tools.executeCommand(args)
# index = index+1
md_tools.pdb2gmx(confFile,"-ff amber99sb-ildn -vsite hydrogens -water tip3p -ignh -o %s"%confFile)
#TODO grep the last line to get charge imbalances
boxSize= pdb_util.findPDBBoxSize(frame)
nonProteinString = pdb_util.findAllNonProtein(frame)
proteinString = pdb_util.findAllAminoAcidLines(confFile)
with open(confFile,"w") as f:
f.write(boxSize)
f.write("\n")
f.write(proteinString)
f.write(nonProteinString)
membrane.injectLinesIntoTop("topol.top")
md_tools.updateMembraneCount("POPC",confFile,"topol.top",fileType="pdb")
md_tools.updateWaterAndIonCount(confFile,"topol.top")
md_tools.cleanupBackups()
os.system("cp protein_mutated.pdb %s"%currentProtein)
print "Done mutating"
logCommand("Mutated protein using the file mutate.pml in root project dir")
if protonationString:
pdb2gmx(currentProtein,pdb2gmxOptions%currentProtein,protonationSelections="-asp -glu -his -arg -lys"
,protonationStates=protonationString)
else:
pdb2gmx(currentProtein,pdb2gmxOptions%currentProtein)
#assuming that the provided files includes the whole system
mergeProteinAndMembranePdb(currentProtein,system)
index+=1
#only need to do this for one topology file
updateMembraneCount("POPC",currentProtein,"topol.top",fileType="pdb")
updateWaterAndIonCount(currentProtein,"topol.top")
injectLinesIntoTop("topol.top")
#TODO
#ensureCorrectSolventOrder(currentProtein,"topol.top")
os.system("mv topol.top *.itp ../")
os.system(r"rm \#* conf*.pdb.* topol.top.*")
print "Done however you need to ensure that the molecule order in the top file is correct and that your system has balanced charges"
