htmd.builder.amber.
build
(mol, ff=None, topo=None, param=None, prefix='structure', outdir='./build', caps=None, ionize=True, saltconc=0, saltanion=None, saltcation=None, disulfide=None, teleap=None, teleapimports=None, execute=True, atomtypes=None, offlibraries=None, gbsa=False, igb=2)¶Builds a system for AMBER
Uses tleap to build a system for AMBER. Additionally it allows the user to ionize and add disulfide bridges.
Parameters: |
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Returns: | molbuilt – The built system in a Molecule object |
Return type: |
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Example
>>> from htmd.ui import *
>>> mol = Molecule("3PTB")
>>> molbuilt = amber.build(mol, outdir='/tmp/build')
>>> # More complex example
>>> disu = [['segid P and resid 157', 'segid P and resid 13'], ['segid K and resid 1', 'segid K and resid 25']]
>>> molbuilt = amber.build(mol, outdir='/tmp/build', saltconc=0.15, disulfide=disu)
htmd.builder.amber.
defaultAmberHome
(teleap=None)¶Returns the default AMBERHOME as defined by the location of teLeap binary
htmd.builder.amber.
defaultFf
()¶Returns the default leaprc forcefield files used by amber.build
htmd.builder.amber.
defaultParam
()¶Returns the default parameter frcmod files used by amber.build
htmd.builder.amber.
defaultTopo
()¶Returns the default topology prepi files used by amber.build
htmd.builder.amber.
htmdAmberHome
()¶Returns the location of the AMBER files distributed with HTMD
htmd.builder.amber.
listFiles
()¶Lists all AMBER forcefield files available in HTMD
Example
>>> from htmd.builder import amber
>>> amber.listFiles()
---- Forcefield files list: ... ----
leaprc.constph
leaprc.DNA.bsc1
leaprc.DNA.OL15
leaprc.ff14SB.redq
...