Unverified Commit 7b4927cf authored by peastman's avatar peastman Committed by GitHub
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Fixed bug in addMembrane() (#2932)

parent 89eec67c
...@@ -6,7 +6,7 @@ Simbios, the NIH National Center for Physics-Based Simulation of ...@@ -6,7 +6,7 @@ Simbios, the NIH National Center for Physics-Based Simulation of
Biological Structures at Stanford, funded under the NIH Roadmap for Biological Structures at Stanford, funded under the NIH Roadmap for
Medical Research, grant U54 GM072970. See https://simtk.org. Medical Research, grant U54 GM072970. See https://simtk.org.
Portions copyright (c) 2012-2018 Stanford University and the Authors. Portions copyright (c) 2012-2020 Stanford University and the Authors.
Authors: Peter Eastman Authors: Peter Eastman
Contributors: Contributors:
...@@ -1223,9 +1223,9 @@ class Modeller(object): ...@@ -1223,9 +1223,9 @@ class Modeller(object):
forcefield : ForceField forcefield : ForceField
the ForceField to use for determining atomic charges and for relaxing the membrane the ForceField to use for determining atomic charges and for relaxing the membrane
lipidType : string or object lipidType : string or object
the type of lipid to use. Supported string values are 'POPC' and 'POPE'. For other types the type of lipid to use. Supported string values are 'POPC', 'POPE', 'DLPC', 'DLPE', 'DMPC',
of lipids, provide a PDBFile or PDBxFile object (or any other object with "topology" and 'DOPC', and 'DPPC'. For other types of lipids, provide a PDBFile or PDBxFile object (or any
"positions" fields) containing a membrane patch. other object with "topology" and "positions" fields) containing a membrane patch.
membraneCenterZ: distance=0*nanometer membraneCenterZ: distance=0*nanometer
the position along the Z axis of the center of the membrane the position along the Z axis of the center of the membrane
minimumPadding : distance=1*nanometer minimumPadding : distance=1*nanometer
...@@ -1375,7 +1375,7 @@ class Modeller(object): ...@@ -1375,7 +1375,7 @@ class Modeller(object):
# Remove the same number of residues from each leaf. # Remove the same number of residues from each leaf.
skipFromLeaf[lipidLeaf[residue]] -= 1 skipFromLeaf[lipidLeaf[residue]] -= 1
else: else:
newResidue = membraneTopology.addResidue(residue.name, lipidChain, lipidResNum, residue.insertionCode) newResidue = membraneTopology.addResidue(residue.name, lipidChain, str(lipidResNum), residue.insertionCode)
lipidResNum += 1 lipidResNum += 1
for atom in residue.atoms(): for atom in residue.atoms():
......
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