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, custombonds=None, remove=None)#

Build a system for AMBER.

Uses tleap to build a system for AMBER. Additionally allows for ionization and adding disulfide bridges.

Parameters:

  • mol (Molecule) – The Molecule object containing the system.

  • ff (list | None) – A list of leaprc forcefield files. Use amber.listFiles to get a list of available forcefield files. If None, uses amber.defaultFf.

  • topo (list | None) – A list of topology prepi/prep/in/cif files. CIF and MOL2 files are automatically converted to mol2 format. Use amber.listFiles to get a list of available topology files. If None, uses amber.defaultTopo. When passing residues parameterized with the parameterize tool, pass the .cif file.

  • param (list | None) – A list of parameter frcmod files. Use amber.listFiles to get a list of available parameter files. If None, uses amber.defaultParam.

  • prefix (str) – The prefix for the generated pdb and prmtop files.

  • outdir (str) – The path to the output directory.

  • caps (dict | None) – A dictionary specifying the caps. Accepts two formats. First format: keys are segids, values are lists of cap strings for that segment. e.g. caps['P'] = ['ACE', 'NME'] or caps['P'] = ['none', 'none']. If None, ACE and NME caps are applied to every protein segment. Second format: keys are atom selection strings for a residue, values are the cap name. e.g. caps = {"chain A and resid 5": "ACE", "chain A and resid 10": "NME"}.

  • ionize (bool) – Enable or disable ionization.

  • saltconc (float) – Salt concentration (in Molar) to add to the system after neutralization.

  • saltanion (str | None) – The anion type. Available: 'Cl-'. Also accepts 'CL', 'chloride', 'CLA'.

  • saltcation (str | None) – The cation type. Available: 'Na+', 'K+', 'Cs+', 'Mg2+', 'Ca2+', 'Zn2+'. Also accepts formats such as 'NA', 'sodium', 'SOD'.

  • disulfide (list | None) – If None, disulfide bonds are guessed automatically. Otherwise provide a list of pairs of atom selection strings for each pair of residues forming a disulfide bridge.

  • teleap (str | None) – Path to the teLeap executable. If None, located automatically from PATH.

  • teleapimports (list | None) – A list of directory paths to pass to teLeap via the -I flag. If None, determined from amber.defaultAmberHome and amber.htmdAmberHome.

  • execute (bool) – If True, run the full build. If False, only write the tleap input script without building. Ionization is skipped when False.

  • atomtypes (list | None) – Custom atom types as a list of ('type', 'element', 'hybrid') triplets, e.g. [('C1', 'C', 'sp2'), ('CI', 'C', 'sp3')]. See addAtomTypes in AmberTools docs.

  • offlibraries (list | str | None) – A path or list of paths to OFF library files. See loadOFF in AmberTools docs.

  • gbsa (bool) – Modify radii for the GBSA implicit water model.

  • igb (int) – GB model: 1 for mbondi, 2 and 5 for mbondi2, 7 for bondi, 8 for mbondi3. See section 4 of the AMBER manual on the Generalized Born/Surface Area model.

  • custombonds (list | None) – A list of pairs of atom selection strings specifying custom bonds to add.

  • remove (list | None) – A list of atom selection strings. Matching atoms or residues are removed from the system. Useful for removing atoms added during building.

Returns:

molbuilt – The built system as a Molecule object.

Return type:

Molecule

Examples

>>> 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)#

Return the default AMBERHOME directory.

Determined from the location of the teLeap binary, or the tleap_pyodide package directory when running in a pyodide environment.

Parameters:

teleap (str | None) – Path to the teLeap executable. If None, the executable is located automatically from PATH.

Returns:

amberhome – The AMBERHOME directory path.

Return type:

str

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.amberdyes
leaprc.conste
leaprc.constph
leaprc.DNA.bsc1
...