htmd.builder.amber module

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:
  • 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.
Returns:

molbuilt – The built system in a Molecule object

Return type:

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

teleap : str
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
...