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tsoc
openmm
Commits
7b4927cf
Unverified
Commit
7b4927cf
authored
Nov 23, 2020
by
peastman
Committed by
GitHub
Nov 23, 2020
Browse files
Fixed bug in addMembrane() (#2932)
parent
89eec67c
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wrappers/python/simtk/openmm/app/modeller.py
wrappers/python/simtk/openmm/app/modeller.py
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wrappers/python/simtk/openmm/app/modeller.py
View file @
7b4927cf
...
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@@ -6,7 +6,7 @@ Simbios, the NIH National Center for Physics-Based Simulation of
Biological Structures at Stanford, funded under the NIH Roadmap for
Medical Research, grant U54 GM072970. See https://simtk.org.
Portions copyright (c) 2012-20
18
Stanford University and the Authors.
Portions copyright (c) 2012-20
20
Stanford University and the Authors.
Authors: Peter Eastman
Contributors:
...
...
@@ -1223,9 +1223,9 @@ class Modeller(object):
forcefield : ForceField
the ForceField to use for determining atomic charges and for relaxing the membrane
lipidType : string or object
the type of lipid to use. Supported string values are 'POPC'
and
'POPE'
. For other types
of lipids, provide a PDBFile or PDBxFile object (or any
other object with "topology" and
"positions" fields) containing a membrane patch.
the type of lipid to use. Supported string values are 'POPC'
,
'POPE'
, 'DLPC', 'DLPE', 'DMPC',
'DOPC', and 'DPPC'. For other types
of lipids, provide a PDBFile or PDBxFile object (or any
other object with "topology" and
"positions" fields) containing a membrane patch.
membraneCenterZ: distance=0*nanometer
the position along the Z axis of the center of the membrane
minimumPadding : distance=1*nanometer
...
...
@@ -1375,7 +1375,7 @@ class Modeller(object):
# Remove the same number of residues from each leaf.
skipFromLeaf
[
lipidLeaf
[
residue
]]
-=
1
else
:
newResidue
=
membraneTopology
.
addResidue
(
residue
.
name
,
lipidChain
,
lipidResNum
,
residue
.
insertionCode
)
newResidue
=
membraneTopology
.
addResidue
(
residue
.
name
,
lipidChain
,
str
(
lipidResNum
)
,
residue
.
insertionCode
)
lipidResNum
+=
1
for
atom
in
residue
.
atoms
():
...
...
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