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tsoc
openmm
Commits
fb8c80ad
"vscode:/vscode.git/clone" did not exist on "8aa0f1f7b1764dda783723c8a2e3f08e2a554e13"
Unverified
Commit
fb8c80ad
authored
Aug 06, 2019
by
peastman
Committed by
GitHub
Aug 06, 2019
Browse files
Merge pull request #2362 from j-wags/fix_2360
Fix 2360
parents
bf7aee53
beb977ae
Changes
2
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2 changed files
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+10
-0
wrappers/python/simtk/openmm/app/internal/amber_file_parser.py
...ers/python/simtk/openmm/app/internal/amber_file_parser.py
+2
-0
wrappers/python/tests/TestAmberPrmtopFile.py
wrappers/python/tests/TestAmberPrmtopFile.py
+8
-0
No files found.
wrappers/python/simtk/openmm/app/internal/amber_file_parser.py
View file @
fb8c80ad
...
@@ -989,6 +989,8 @@ def readAmberSystem(topology, prmtop_filename=None, prmtop_loader=None, shake=No
...
@@ -989,6 +989,8 @@ def readAmberSystem(topology, prmtop_filename=None, prmtop_loader=None, shake=No
gb
=
mm
.
GBSAOBCForce
()
gb
=
mm
.
GBSAOBCForce
()
gb
.
setSoluteDielectric
(
soluteDielectric
)
gb
.
setSoluteDielectric
(
soluteDielectric
)
gb
.
setSolventDielectric
(
solventDielectric
)
gb
.
setSolventDielectric
(
solventDielectric
)
if
gbsaModel
is
None
:
gb
.
setSurfaceAreaEnergy
(
0
)
elif
gbmodel
==
'GBn'
:
elif
gbmodel
==
'GBn'
:
gb
=
customgb
.
GBSAGBnForce
(
solventDielectric
,
soluteDielectric
,
gbsaModel
,
cutoff
,
implicitSolventKappa
)
gb
=
customgb
.
GBSAGBnForce
(
solventDielectric
,
soluteDielectric
,
gbsaModel
,
cutoff
,
implicitSolventKappa
)
elif
gbmodel
==
'GBn2'
:
elif
gbmodel
==
'GBn2'
:
...
...
wrappers/python/tests/TestAmberPrmtopFile.py
View file @
fb8c80ad
...
@@ -127,6 +127,14 @@ class TestAmberPrmtopFile(unittest.TestCase):
...
@@ -127,6 +127,14 @@ class TestAmberPrmtopFile(unittest.TestCase):
self
.
assertTrue
(
found_matching_solvent_dielectric
and
self
.
assertTrue
(
found_matching_solvent_dielectric
and
found_matching_solute_dielectric
)
found_matching_solute_dielectric
)
def
test_ImplicitSolventZeroSA
(
self
):
"""Test that requesting gbsaModel=None yields a surface area energy of 0 when
prmtop.createSystem produces a GBSAOBCForce"""
system
=
prmtop2
.
createSystem
(
implicitSolvent
=
OBC2
,
gbsaModel
=
None
)
for
force
in
system
.
getForces
():
if
isinstance
(
force
,
GBSAOBCForce
):
self
.
assertEqual
(
force
.
getSurfaceAreaEnergy
(),
0
*
kilojoule
/
(
nanometer
**
2
*
mole
))
def
test_HydrogenMass
(
self
):
def
test_HydrogenMass
(
self
):
"""Test that altering the mass of hydrogens works correctly."""
"""Test that altering the mass of hydrogens works correctly."""
...
...
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