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pdbfixer
Commits
6c59d383
Commit
6c59d383
authored
Nov 24, 2020
by
peastman
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Support all lipid types from OpenMM 7.5
parent
fe4e73b6
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8 additions
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3 deletions
+8
-3
pdbfixer/html/addHydrogens.html
+5
-0
pdbfixer/pdbfixer.py
+3
-3
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pdbfixer/html/addHydrogens.html
View file @
6c59d383
...
...
@@ -159,6 +159,11 @@ Add a water box or membrane surrounding the model?
<select
id=
"lipidType"
name=
"lipidType"
>
<option
value=
"POPC"
selected=
"selected"
>
POPC
</option>
<option
value=
"POPE"
>
POPE
</option>
<option
value=
"DLPC"
>
DLPC
</option>
<option
value=
"DLPE"
>
DLPE
</option>
<option
value=
"DMPC"
>
DMPC
</option>
<option
value=
"DOPC"
>
DOPC
</option>
<option
value=
"DPPC"
>
DPPC
</option>
</select>
<p>
Minimum padding around protein:
<input
type=
"text"
id=
"membranePadding"
name=
"membranePadding"
value=
"1.0"
size=
"5"
>
(nm)
...
...
pdbfixer/pdbfixer.py
View file @
6c59d383
...
...
@@ -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) 2013-20
15
Stanford University and the Authors.
Portions copyright (c) 2013-20
20
Stanford University and the Authors.
Authors: Peter Eastman
Contributors:
...
...
@@ -30,7 +30,7 @@ USE OR OTHER DEALINGS IN THE SOFTWARE.
"""
from
__future__
import
absolute_import
__author__
=
"Peter Eastman"
__version__
=
"1.
6
"
__version__
=
"1.
7
"
import
simtk.openmm
as
mm
import
simtk.openmm.app
as
app
...
...
@@ -1098,7 +1098,7 @@ class PDBFixer(object):
Parameters
----------
lipidType : string='POPC'
the type of lipid to use. Supported values are 'POPC'
and 'POPE
'.
the type of lipid to use. Supported values are 'POPC'
, 'POPE', 'DLPC', 'DLPE', 'DMPC', 'DOPC', and 'DPPC
'.
membraneCenterZ: distance=0*nanometer
the position along the Z axis of the center of the membrane
minimumPadding : distance=1*nanometer
...
...
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