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Added ability to calculate non-neutral charges #23

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Added ability to calculate non-neutral charges #23

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590b262
Added ability to calculate non-neutral charges
jingjieyeo May 30, 2019
b53fe5f
Merge pull request #1 from jingjieyeo/jingjieyeo-patch-1
jingjieyeo May 30, 2019
0b8d596
Update dreiding.py for polar hydrogen
jingjieyeo Jul 16, 2019
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6 changes: 3 additions & 3 deletions pysimm/amber.py
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Original file line number Diff line number Diff line change
Expand Up @@ -63,10 +63,10 @@ def cleanup_antechamber():
print('problem removing {} during cleanup'.format(fname))


def calc_charges(s, charge_method='bcc', cleanup=True):
def calc_charges(s, charge_method='bcc', net_charge='0', cleanup=True):
"""pysimm.amber.calc_charges

Calculates charges using antechamber. Defaults to am1-bcc charges.
Calculates charges using antechamber. Defaults to am1-bcc charges and neutral charge.

Args:
s: System for which to calculate charges. System object is updated in place
Expand All @@ -77,7 +77,7 @@ def calc_charges(s, charge_method='bcc', cleanup=True):
None
"""
s.write_pdb('pysimm.tmp.pdb')
cl = '{} -fi pdb -i pysimm.tmp.pdb -fo ac -o pysimm.tmp.ac -c {}'.format(ANTECHAMBER_EXEC, charge_method)
cl = '{} -fi pdb -i pysimm.tmp.pdb -fo ac -o pysimm.tmp.ac -c {} -nc {}'.format(ANTECHAMBER_EXEC, charge_method, net_charge)
p = Popen(cl.split(), stdin=PIPE, stdout=PIPE, stderr=PIPE)
p.communicate()
with file('pysimm.tmp.ac') as f:
Expand Down
8 changes: 6 additions & 2 deletions pysimm/forcefield/dreiding.py
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Original file line number Diff line number Diff line change
Expand Up @@ -86,7 +86,11 @@ def assign_ptypes(self, s):
p.nbonds += 1
for p in s.particles:
if p.elem == 'H':
p.type_name = 'H_'
for pb in p.bonded_to:
if pb.elem == 'O' or pb.elem == 'N':
p.type_name = 'H___A'
if not p.type_name:
p.type_name = 'H_'
elif p.elem == 'C':
if p.bond_orders and (4 in p.bond_orders or 'A' in p.bond_orders):
p.type_name = 'C_R'
Expand Down Expand Up @@ -357,4 +361,4 @@ def assign_charges(self, s, charges='gasteiger'):
"""
if charges == 'gasteiger':
print('adding gasteiger charges')
gasteiger.set_charges(s)
gasteiger.set_charges(s)