pele.amber.amberSystem#

System class for biomolecules using AMBER ff.

Set up using prmtop and inpcrd files used in Amber GMIN and Optim.

Potential parameters (e.g. non-bonded cut-offs are set in

TODO:

Parameters#

prmtopFname : str prmtop file name

inpcrdFname : str inpcrd file name

BaseSystem

AMBERSystem.set_params()

Source

def set_params(self, params):

set default parameters for the system

AMBERSystem.get_potential()

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def get_potential(self):

First attempts to get the potential from GMIN, then from OpenMM. If both fail, sets it to None

AMBERSystem.get_random_configuration()

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def get_random_configuration(self):

set coordinates before calling BH etc.

AMBERSystem.get_metric_tensor()

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def get_metric_tensor(self, coords):

metric tensor for all masses m_i=1.0

AMBERSystem.load_coords_pymol()

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def load_coords_pymol(self, coordslist, oname, index=1):

load the coords into pymol

the new object must be named oname so we can manipulate it later

Parameters:

coordslistlist of arrays
onamestr: the new pymol object must be named oname so it can be manipulated later
indexint: we can have more than one molecule on the screen at one time. index tells which one to draw. They are viewed at the same time, so should be visually distinct, e.g. different colors. accepted values are 1 or 2

Notes

the implementation here is a bit hacky. we create a temporary xyz file from coords and load the molecule in pymol from this file.

AMBERSystem.check_cistrans()

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def check_cistrans(self, coords):

Sanity check on the isomer state of peptide bonds

Returns False if the check fails i.e. if any of the peptide bond is CIS

AMBERSystem.check_CAchirality()

Source

def check_CAchirality(self, coords):

Sanity check on the CA to check if it is L of D

Returns False if the check fails i.e. if any D-amino acid is present

AMBERSystem.test_potential()

Source

def test_potential(self, pdbfname):

tests amber potential for pdbfname

Input
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    pdbfname = full path to pdb file