def perturb_parameters(perturb, hmr, prmtop):
"""
Use ParmEd to make parameter perturbations
"""
new_param = prmtop
parm = AmberParm(prmtop + '.prmtop')
logfile = open('parmed.log', 'w')
if perturb == 'yes':
# Parsing the input file that includes new parameters
with open('new_params.dat') as fr:
lines = fr.read().splitlines()
lines = list(line for line in lines if line) # Remove blank lines
for line in lines:
if not line[0] == ';':
splitline = line.split()
if len(splitline) < 4:
print 'Aborted. Wrong format! Please provide atom type(e.g.,OW), parameter type(e.g.,vdw), and the corresponding radius/epsilon parameters '
print '(separated with spaces.)\n'
atom_type = splitline[0]
param_type = splitline[1]
radius = splitline[2]
epsilon = splitline[3]
if param_type.lower() == 'vdw':
action = changeLJSingleType(parm, "@%" + atom_type, radius,
epsilon)
action.execute()
logfile.write(('%s\n' % action))
else:
print 'Aborted. Only the feauture of perturbing vdW parameters is supported for now.\n'
sys.exit(1)
new_param += '.perturbed'
if os.path.isfile(new_param + '.prmtop'):
os.remove(new_param + '.prmtop')
Structure.save(parm, new_param + '.prmtop')
if hmr == 'yes':
parm = AmberParm(new_param + '.prmtop')
# Use the ParmEd API, which is more stable than calling a subprocess
action = HMassRepartition(parm)
action.execute()
logfile.write(('%s\n' % action))
new_param += '.hmr'
if os.path.isfile(new_param + '.prmtop'):
os.remove(new_param + '.prmtop')
Structure.save(parm, new_param + '.prmtop')
return new_param
def parmed_topology(top_file, param_type, param_list, TIP3P_param_list, index):
"""
Use ParmEd to edit water parameters
"""
parm = AmberParm(top_file)
local_param_list = TIP3P_param_list
ow_charge_column = hw_charge_column = ow_rad_column = ow_eps_column = 999
# Write a log file for parmEd
f = open('waterbot_parmed.log', 'w')
logfile = open('parmed.log', 'w')
for i, nonbonded_term in enumerate(param_type):
if 'charge' in nonbonded_term.lower() and 'ow' in nonbonded_term.lower(
):
ow_charge_column = i
f.write('The partial charge of water oxygen will be perturbed; ')
f.write('the value of the new parameter is %.4f.\n' %
(param_list[i][index]))
local_param_list[2] = param_list[i][index]
elif 'charge' in nonbonded_term.lower(
) and 'hw' in nonbonded_term.lower():
hw_charge_column = i
f.write('The partial charge of water hydrogen will be perturbed; ')
f.write('the value of the new parameter is %.4f.\n' %
(param_list[i][index]))
local_param_list[3] = param_list[i][index]
elif 'radius' in nonbonded_term.lower():
ow_rad_column = i
f.write(
'The radii parameter of water hydrogen will be perturbed; ')
f.write('the value of the new parameter is %.4f.\n' %
(param_list[i][index]))
local_param_list[0] = param_list[i][index]
elif 'epsilon' in nonbonded_term.lower():
ow_eps_column = i
f.write(
'The epsilon parameter of water hydrogen will be perturbed; ')
f.write('the value of the new parameter is %.4f.\n' %
(param_list[i][index]))
local_param_list[1] = param_list[i][index]
# if only one of the charges were provided:
if ow_charge_column == 999 and hw_charge_column != 999:
f.write('\nThe charge of water oxygen was not provided.')
local_param_list[2] = -2.0 * local_param_list[3]
f.write(
'A value of %.4f was computed and used to make sure this water model is neutral.'
% (local_param_list[2]))
elif hw_charge_column == 999 and ow_charge_column != 999:
f.write('\nThe charge of water hydrogen was not provided.')
local_param_list[3] = -local_param_list[2] / 2.0
f.write(
'A value of %.4f was computed and used to make sure this water model is neutral.'
% (local_param_list[3]))
# Check whether the water model has a neutral charge
if (local_param_list[2] + 2 * local_param_list[3]) != 0:
f.write('\nAborted.The new water model is not neutral!!!\n')
sys.exit(1)
if ow_rad_column != 999 or ow_eps_column != 999:
# It looks like there is no way to only change radius or epsilon
action = changeLJSingleType(parm, "@%OW", local_param_list[0],
local_param_list[1])
action.execute()
logfile.write(('%s\n' % action))
if ow_charge_column != 999 or hw_charge_column != 999:
action = change(parm, 'CHARGE', "@%OW", local_param_list[2])
action.execute()
logfile.write(('%s\n' % action))
Structure.save(parm, 'solvated_perturbed.prmtop')
