acelleralivehtmd.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.
mol (Molecule object) – The Molecule object containing the system
ff (list of str) – A list of leaprc forcefield files.
Use amber.listFiles to get a list of available forcefield files.
Default: amber.defaultFf
topo (list of str) – A list of topology prepi/prep/in files.
Use amber.listFiles to get a list of available topology files.
Default: amber.defaultTopo
param (list of str) – A list of parameter frcmod files.
Use amber.listFiles to get a list of available parameter files.
Default: amber.defaultParam
prefix (str) – The prefix for the generated pdb and psf files
outdir (str) – The path to the output directory Default: ‘./build’
caps (dict) – A dictionary with keys segids and values lists of strings describing the caps for a particular protein segment. e.g. caps[‘P’] = [‘ACE’, ‘NME’] or caps[‘P’] = [‘none’, ‘none’]. Default: will apply ACE and NME caps to every protein segment.
ionize (bool) – Enable or disable ionization
saltconc (float) – Salt concentration to add to the system after neutralization.
saltanion ({'Cl-'}) – The anion type. Please use only AMBER ion atom names.
saltcation ({'Na+', 'K+', 'Cs+'}) – The cation type. Please use only AMBER ion atom names.
disulfide (list of pairs of atomselection strings) – If None it will guess disulfide bonds. Otherwise provide a list pairs of atomselection strings for each pair of residues forming the disulfide bridge.
teleap (str) – Path to teLeap executable used to build the system for AMBER
teleapimports (list) – A list of paths to pass to teLeap ‘-I’ flag, i.e. directories to be searched
Default: determined from amber.defaultAmberHome and
amber.htmdAmberHome
execute (bool) – Disable building. Will only write out the input script needed by tleap. Does not include ionization.
atomtypes (list of triplets) – Custom atom types defined by the user as (‘type’, ‘element’, ‘hybrid’) triplets e.g. ((‘C1’, ‘C’, ‘sp2’), (‘CI’, ‘C’, ‘sp3’)). Check addAtomTypes in AmberTools docs.
offlibraries (str or list) – A path or a list of paths to OFF library files. Check loadOFF in AmberTools docs.
gbsa (bool) – Modify radii for GBSA implicit water model
igb (int) – GB model. Select: 1 for mbondi, 2 and 5 for mbondi2, 7 for bondi and 8 for mbondi3. Check section 4. The Generalized Born/Surface Area Model of the AMBER manual.
molbuilt – The built system in a Molecule object
Molecule object
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
Path to teLeap executable used to build the system for AMBER
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
...