def add_ions(neutral=True, conc=0, pname='NA', nname='CL'):
if (not neutral) and (conc == 0):
utils.update("add_ions", "no ions will be added...")
return
if neutral:
utils.update("add_ions", "will add ions ({}/{}) to neutralize the system...".format(pname, nname))
if conc > 0:
utils.update("add_ions", "will add ions ({}/{}) for target concentration = {} mmol/ml...".format(pname, nname, conc))
# Generate IONS.mdp (just a dummy required).
os.system('touch IONS.mdp')
# Add ion topology to topol.top.
topol.add_mol("{0}.ff/ions.itp".format(universe.get('d_modelFF')), "Include ion topology")
# Run gmx grompp and genion.
utils.update("add_ions", "running gmx grompp and genion to add ions...")
os.system("gmx grompp -f IONS.mdp -c {0} -p topol.top -o IONS.tpr >> builder.log 2>&1".format(universe.get('d_nameList')[-1]))
if neutral:
os.system("gmx genion -s IONS.tpr -o {0}_ION.pdb -p topol.top -pname {1} -nname {2} -conc {3} -neutral >> builder.log 2>&1 << EOF\nSOL\nEOF".format(universe.get('d_pdbName'), pname, nname, conc))
else:
os.system("gmx genion -s IONS.tpr -o {0}_ION.pdb -p topol.top -pname {1} -nname {2} -conc {3} >> builder.log 2>&1 << EOF\nSOL\nEOF".format(universe.get('d_pdbName'), pname, nname, conc))
# To update d_residues.
load("{0}_ION.pdb".format(universe.get('d_pdbName')))
# To update d_nameList.
utils.add_to_nameList("{0}_ION.pdb".format(universe.get('d_pdbName')))
def write(name):
with open(name, 'w') as file:
if universe.has('d_title'):
file.write("TITLE {0}\n".format(universe.get('d_title')))
if universe.has('d_box'):
file.write("CRYST1{0}\n".format(universe.get('d_box')))
file.write("MODEL {:8d}\n".format(universe.get('d_model')))
atomNumber = 1
for residue in universe.get('d_residues'):
for idx in range(0, len(residue.d_atoms)):
file.write(
"{:6s}{:5d} {:^4s}{:1s}{:4s}{:1s}{:4d}{:1s} {:8.3f}{:8.3f}{:8.3f}\n"
.format('ATOM', atomNumber, residue.d_atoms[idx],
residue.d_ali[idx], residue.d_resname,
residue.d_chain, residue.d_resid, '',
residue.d_x[idx], residue.d_y[idx],
residue.d_z[idx]))
atomNumber += 1
file.write("TER\nENDMDL\n")
utils.add_to_nameList(name)
def energy_minimize():
gen_mdp('EM')
utils.update("energy_minimize",
"running gmx grompp and mdrun for energy minimization...")
os.system(
"gmx grompp -f EM.mdp -c {0} -p topol.top -o EM.tpr -r {0} >> builder.log 2>&1"
.format(universe.get('d_nameList')[-1]))
os.system("gmx mdrun -deffnm EM -c EM.pdb >> builder.log 2>&1")
utils.add_to_nameList("EM.pdb")
def energy_pcouple():
gen_mdp('NPT')
utils.update("energy_pcouple",
"running gmx grompp and mdrun for pressure coupling...")
os.system(
"gmx grompp -f NPT.mdp -c {0} -p topol.top -o NPT.tpr -r {0} >> builder.log 2>&1"
.format(universe.get('d_nameList')[-1]))
os.system("gmx mdrun -deffnm NPT -c NPT.pdb >> builder.log 2>&1")
utils.add_to_nameList("NPT.pdb")
def add_water():
utils.update("add_water", "running gmx solvate...")
os.system("gmx solvate -cp {0} -o {1}_SOL.pdb >> builder.log 2>&1".format(universe.get('d_nameList')[-1], universe.get('d_pdbName')))
# To update d_residues.
load("{0}_SOL.pdb".format(universe.get('d_pdbName')))
# To update topol.top.
topol.add_mol("{0}.ff/{1}.itp".format(universe.get('d_modelFF'), universe.get('d_modelWater')), "Include water topology", "SOL", countRes('SOL'))
# To update d_nameList.
utils.add_to_nameList("{0}_SOL.pdb".format(universe.get('d_pdbName')))
def energy_tcouple():
gen_mdp('NVT')
utils.update("energy_tcouple",
"running gmx grompp and mdrun for temperature coupling...")
os.system(
"gmx grompp -f NVT.mdp -c {0} -p topol.top -o NVT.tpr -r {0} >> builder.log 2>&1"
.format(universe.get('d_nameList')[-1]))
os.system(
"gmx mdrun -deffnm NVT -c {0}_NVT.pdb >> builder.log 2>&1".format(
universe.get('d_pdbName')))
utils.add_to_nameList("{0}_NVT.pdb".format(universe.get('d_pdbName')))
def add_box(d_boxMargin, d_boxType='cubic'):
utils.update("add_box", "adding box using gmx editconf (boxMargin = {0}, boxType = {1})...".format(d_boxMargin, d_boxType))
os.system("gmx editconf -f {0} -o {1}_BOX.pdb -d {2} -bt {3} >> builder.log 2>&1".format(universe.get('d_nameList')[-1], universe.get('d_pdbName'), d_boxMargin, d_boxType))
# To set d_boxMargin and d_boxType.
universe.add('d_boxMargin', d_boxMargin)
universe.add('d_boxType', d_boxType)
# To update d_box.
load("{0}_BOX.pdb".format(universe.get('d_pdbName')))
# To update d_nameList.
utils.add_to_nameList("{0}_BOX.pdb".format(universe.get('d_pdbName')))
def add_buffer(ph_bufpdbName, ph_bufitpName, ph_bufMargin=2.0, ph_bufnmol=-1, attempts=100000):
if not (universe.get('ph_constantpH') and universe.get('ph_restrainpH')):
utils.update("add_buffer", "either ph_constantpH or ph_restrainpH is False --> skipping...")
return
# If user doesn't specified the amount, use #BUF = #ACID.
if (ph_bufnmol == -1):
ph_bufnmol = countRes('ASP') + countRes('GLU')
utils.update("add_buffer", "will attempt to add {0} buffer molecule(s)...".format(ph_bufnmol))
# RUN GROMACS INSERT-MOLECULES COMMAND
os.system("touch vdwradii.dat") # we need this dummy file for this to work.
os.system("gmx insert-molecules -f {0} -o {1}_BUF.pdb -ci {2} -nmol {3} -scale 1.0 -radius {4} -try {5} >> builder.log 2>&1".format(
universe.get('d_nameList')[-1],
universe.get('d_pdbName'),
ph_bufpdbName,
ph_bufnmol,
0.5 * ph_bufMargin,
int(attempts / ph_bufnmol)))
os.remove("vdwradii.dat") # clean dummy file.
# To update d_residues.
load("{0}_BUF.pdb".format(universe.get('d_pdbName')))
# Give user a warning if there wasn't enough space.
actual = countRes('BUF')
if actual < ph_bufnmol:
utils.update("add_buffer", "warning: only {0}/{1} requested buffer molecules inserted after {2} attempts,".format(actual, ph_bufnmol, attempts))
utils.update("add_buffer", "warning: try decreasing ph_bufMargin (={0}nm) or increasing d_boxMargin (={1}nm)...".format(ph_bufMargin, universe.get('d_boxMargin')))
else:
utils.update("add_buffer", "succesfully added {0} buffer molecule(s)...".format(actual))
# To add buffer topology to topol.top.
utils.update("add_buffer", "updating topology...")
os.system("cp {} .".format(ph_bufitpName))
topol.add_mol(os.path.basename(ph_bufitpName), "Include buffer topology", 'BUF', actual)
# Set some parameters in the universe.
universe.add('ph_bufpdbName', ph_bufpdbName)
universe.add('ph_bufitpName', ph_bufitpName)
universe.add('ph_bufMargin', ph_bufMargin)
universe.add('ph_bufnmol', actual)
# To update d_nameList.
utils.add_to_nameList("{0}_BUF.pdb".format(universe.get('d_pdbName')))
def generate(d_modelFF, d_modelWater, d_terministring="", d_customitp=""):
# Internal helper function.
def rebuild_topol():
# If we have only one chain, gromacs will put everything in topol.top.
# If we have more than one chain, gromacs will do it for us.
if (len(universe.get('d_chain')) <= 1):
readingProtein = False
file = open("topol_Protein_chain_A.itp", 'w')
for line in open("topol.top").readlines():
if (not readingProtein and line == "[ moleculetype ]\n"):
readingProtein = True
if (readingProtein and line == "; Include water topology\n"):
readingProtein = False
if (readingProtein):
file.write(line)
file.close()
with open('topol.top', 'w') as file:
file.write("; Include forcefield parameters\n")
file.write("#include \"{0}.ff/forcefield.itp\"\n\n".format(universe.get('d_modelFF')))
file.write("; Include protein topology\n")
for letter in universe.get('d_chain'):
file.write("#include \"topol_Protein_chain_{0}.itp\"\n".format(letter))
file.write('\n')
file.write('[ system ]\n')
file.write('{0}\n\n'.format(universe.get('d_pdbName')))
file.write('[ molecules ]\n')
file.write('; Compounts \t\t #mols\n')
for letter in universe.get('d_chain'):
file.write("Protein_chain_{0}\t\t1\n".format(letter))
# ADD RELEVANT PARAMETERS TO UNIVERSE ######################################
universe.add('d_modelFF', d_modelFF)
universe.add('d_modelWater', d_modelWater)
universe.add('d_terministring', d_terministring)
# USER UPDATE STUFF ########################################################
countACID = protein.countRes("ASP") + protein.countRes("GLU")
# If constant-pH is on,
if universe.get('ph_constantpH'):
utils.update("generate", 'constant-pH is turned on...')
# and we have at least one protonatable reside,
if countACID > 0:
utils.update("generate", "detected {} acidic residue(s):".format(countACID))
for letter in universe.get('d_chain'):
count = 1
for residue in universe.get('d_residues'):
if residue.d_chain == letter:
count += 1
if residue.d_resname in ['ASP', 'GLU']:
utils.update("generate", "{:3s}-{:<4d} in chain {}".format(residue.d_resname, count, letter))
utils.update("generate", "(setting protonation state to true (option 1) for all of these)")
else:
utils.update("generate", "no acidic residues detected, constant-pH is turned off...")
universe.add('ph_constantpH', False)
universe.add('ph_restrainpH', False)
else:
utils.update("generate", 'constant-pH is turned off...')
universe.add('ph_restrainpH', False) # If ph_constantpH is False then this is also False.
utils.update("generate", "using the {} force field with the {} water model...".format(d_modelFF, d_modelWater))
# CREATE EOFSTRING FOR PDB2GMX COMMAND #####################################
# Here we create EOFstring to circumvent pd2gmx prompting for user input.
xstr = "<< EOF"
# The for-loop sets the protonation state of all GLUs and ASPs to 1
# (True) if ph_constantpH is True, and to 0 (False) if ph_constantpH is False.
for chain in universe.get('d_chain'):
for residue in universe.get('d_residues'):
if residue.d_resname in ['ASP', 'GLU'] and residue.d_chain == chain:
xstr += "\n{:d}".format(universe.get('ph_constantpH'))
# Furthermore, if the user specified a two-letter string for the termini,
# add those to the EOFstring as well:
if (d_terministring != ""):
xstr += "\n{}".format(d_terministring[0])
xstr += "\n{}".format(d_terministring[1])
# End EOFstring:
xstr += "\nEOF"
# print(xstr) # Debug
# UPDATE USER ABOUT WHAT WE DO WITH THE TERMINI ############################
if (d_terministring != ""):
utils.update("generate", "Using options {} for termini...".format(d_terministring))
else:
utils.update("generate", "No termini specified, using gmx default (00 = NH3+ and COO-)...")
utils.update("generate", "running pdb2gmx to create {}_PR2.pdb and topol.top...".format(universe.get('d_pdbName')))
# RUN ACTUAL PDB2GMX COMMAND ###############################################
if (d_terministring != ""):
os.system("gmx pdb2gmx -f {0} -o {1}_PR2.pdb -asp -glu -ignh -ff {2} -water {3} -ter >> builder.log 2>&1 {4}".format(universe.get('d_nameList')[-1], universe.get('d_pdbName'), d_modelFF, d_modelWater, xstr))
else:
os.system("gmx pdb2gmx -f {0} -o {1}_PR2.pdb -asp -glu -ignh -ff {2} -water {3} >> builder.log 2>&1 {4}".format(universe.get('d_nameList')[-1], universe.get('d_pdbName'), d_modelFF, d_modelWater, xstr))
# Rebuild topology.
rebuild_topol()
# Use custom topol_Protein_chain_A.itp (this is a temporary fix for charmm36-mar2019-m4)
if (d_customitp != ""):
utils.update("generate", "Overwriting topol_Protein_chain_A.itp generated by pdb2gmx with {}...".format(d_customitp))
os.system("cp {} .".format(d_customitp))
# To update d_residues.
protein.load("{0}_PR2.pdb".format(universe.get('d_pdbName')))
# To update d_nameList.
utils.add_to_nameList("{0}_PR2.pdb".format(universe.get('d_pdbName')))
def add_buffer(ph_bufpdbName="",
ph_bufitpName="",
ph_bufqqA=[1],
ph_bufqqB=[0],
ph_bufMargin=2.5,
attempts=100000):
# This function writes a dummy .pdb containing the default buffer (ion).
def writeDefaultPDB():
with open("defaultBuffer.pdb", 'w') as file:
file.write("TITLE BUFFER PARTICLE\n")
file.write("MODEL 1\n")
file.write(
"ATOM 1 NA BUF 1 110.896 2.872 68.855 1.00 0.00 \n"
)
file.write("TER\n")
file.write("ENDMDL\n")
# This function writes the topology for the default buffer (ion).
# Note: charge should not be 0 because then some interactions are not generated???
# Update: this was fixed by Berk in e2c2340.
def writeDefaultITP():
with open("defaultBuffer.itp", 'w') as file:
file.write("[ moleculetype ]\n")
file.write("; molname nrexcl\n")
file.write("BUF 1\n\n")
file.write("[ atoms ]\n")
file.write(
"; id at type res nr residu name at name cg nr charge \n")
file.write("1 SOD 1 BUF NA 1 0 \n\n")
file.write("#ifdef POSRES_BUF\n")
file.write("; Position restraint for each buffer ion\n")
file.write("[ position_restraints ]\n")
file.write("; i funct fcx fcy fcz\n")
file.write(" 1 1 1000 1000 1000\n")
file.write("#endif\n")
# Skip this whole step if we don't need it.
if not (universe.get('ph_constantpH')
and universe.get('ph_QQleveling') in [1, 2]):
utils.update(
"add_buffer",
"either ph_constantpH is False or ph_QQleveling = 0 --> skipping..."
)
return
# Make sure that the sum of the charges in state A and B are correct.
if (sum(ph_bufqqA) != 1 or sum(ph_bufqqB) != 0):
utils.warning(
"add_buffer",
"buffer charges incorrectly specified! sums must be 1 and 0")
universe.get('ph_bufqqA')
universe.get('ph_bufqqB')
# Determine whether we use the default or a custom buffer.
useDefault = False
if (ph_bufpdbName == "" and ph_bufitpName == ""):
utils.update("add_buffer", "using default (built-in) buffer...")
useDefault = True
elif (ph_bufpdbName == "" and ph_bufitpName != ""):
utils.warning(
"add_buffer",
"ph_bufitpName not specified, resorting to default buffer!")
useDefault = True
elif (ph_bufpdbName != "" and ph_bufitpName == ""):
utils.warning(
"add_buffer",
"ph_bufpdbName not specified, resorting to default buffer!")
useDefault = True
else:
utils.update("add_buffer", "using custom buffer...")
if (useDefault):
# Check to make sure that the charges for the default buffer are correct.
if (ph_bufqqA != [1] or ph_bufqqB != [0]):
utils.warning(
"add_buffer",
"buffer charges incorrectly specified for default buffer!")
universe.get('ph_bufqqA')
universe.get('ph_bufqqB')
# Generate the files for the default buffer and update data members.
writeDefaultPDB()
ph_bufpdbName = "defaultBuffer.pdb"
writeDefaultITP()
ph_bufitpName = "defaultBuffer.itp"
# Get the number of buffer molecules we need.
ph_bufnmol = 0
for lambdaType in universe.get('ph_lambdaTypes'):
ph_bufnmol += countRes(lambdaType.d_resname)
utils.update(
"add_buffer",
"will attempt to add {0} buffer molecule(s)...".format(ph_bufnmol))
# RUN GROMACS INSERT-MOLECULES COMMAND
os.system(
"touch vdwradii.dat") # we need this dummy file for this to work.
os.system(
"gmx insert-molecules -f {0} -o {1}_BUF.pdb -ci {2} -nmol {3} -scale 1.0 -radius {4} -try {5} >> builder.log 2>&1"
.format(
universe.get('d_nameList')[-1], universe.get('d_pdbName'),
ph_bufpdbName, ph_bufnmol, 0.5 * ph_bufMargin,
int(attempts / ph_bufnmol)))
os.remove("vdwradii.dat") # clean dummy file.
# To update d_residues.
load("{0}_BUF.pdb".format(universe.get('d_pdbName')))
# Give user a warning if there wasn't enough space.
actual = countRes('BUF')
if actual < ph_bufnmol:
utils.warning(
"add_buffer",
"only {0}/{1} requested buffer molecules inserted after {2} attempts,"
.format(actual, ph_bufnmol, attempts))
utils.warning(
"add_buffer",
"try decreasing ph_bufMargin (={0}nm) or increasing d_boxMargin (={1}nm)..."
.format(ph_bufMargin, universe.get('d_boxMargin')))
else:
utils.update(
"add_buffer",
"succesfully added {0} buffer molecule(s)...".format(actual))
# To add buffer topology to topol.top.
utils.update("add_buffer", "updating topology...")
if (useDefault):
os.remove("defaultBuffer.pdb") # Remove dummy .pdb file.
else:
os.system("cp {} .".format(ph_bufitpName)) # Copy to working dir.
topol.add_mol(os.path.basename(ph_bufitpName), "Include buffer topology",
'BUF', actual)
# Set some parameters in the universe.
universe.add('ph_bufpdbName', ph_bufpdbName)
universe.add('ph_bufitpName', ph_bufitpName)
universe.add('ph_bufqqA', ph_bufqqA)
universe.add('ph_bufqqB', ph_bufqqB)
universe.add('ph_bufMargin', ph_bufMargin)
universe.add('ph_bufnmol', actual)
# To update d_nameList.
utils.add_to_nameList("{0}_BUF.pdb".format(universe.get('d_pdbName')))