Commit 39267487 authored by Peter Eastman's avatar Peter Eastman
Browse files

Minor fixes

parent d71e72fd
...@@ -94,7 +94,7 @@ class AmberPrmtopFile(object): ...@@ -94,7 +94,7 @@ class AmberPrmtopFile(object):
try: try:
element = elem.get_by_symbol(atomName[0]) element = elem.get_by_symbol(atomName[0])
except KeyError: except KeyError:
pass element = None
top.addAtom(atomName, element, r) top.addAtom(atomName, element, r)
# Add bonds to the topology # Add bonds to the topology
......
...@@ -249,7 +249,7 @@ class ForceField(object): ...@@ -249,7 +249,7 @@ class ForceField(object):
- nonbondedMethod (object=NoCutoff) The method to use for nonbonded interactions. Allowed values are - nonbondedMethod (object=NoCutoff) The method to use for nonbonded interactions. Allowed values are
NoCutoff, CutoffNonPeriodic, CutoffPeriodic, Ewald, or PME. NoCutoff, CutoffNonPeriodic, CutoffPeriodic, Ewald, or PME.
- nonbondedCutoff (distance=1*nanometer) The cutoff distance to use for nonbonded interactions - nonbondedCutoff (distance=1*nanometer) The cutoff distance to use for nonbonded interactions
- constraints (object=None) Specifies which bonds angles should be implemented with constraints. - constraints (object=None) Specifies which bonds and angles should be implemented with constraints.
Allowed values are None, HBonds, AllBonds, or HAngles. Allowed values are None, HBonds, AllBonds, or HAngles.
- rigidWater (boolean=True) If true, water molecules will be fully rigid regardless of the value passed for the constraints argument - rigidWater (boolean=True) If true, water molecules will be fully rigid regardless of the value passed for the constraints argument
- removeCMMotion (boolean=True) If true, a CMMotionRemover will be added to the System - removeCMMotion (boolean=True) If true, a CMMotionRemover will be added to the System
......
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