htmd.builder.amber module#, 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/mol2/cif files. Use amber.listFiles to get a list of available topology files. Default: amber.defaultTopo When passing residues parameterized with the parameterize tool, please pass the .cif file.

  • 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 specifying the caps. It accepts two different formats. One 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. The second format is more manual and uses as keys an atomselection of a residue and as values the cap to apply to that residue. 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 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

Return type:

Molecule object


>>> from htmd.ui import *  
>>> mol = Molecule("3PTB")
>>> molbuilt =, 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 =, outdir='/tmp/build', saltconc=0.15, disulfide=disu)  

Returns the default AMBERHOME as defined by the location of teLeap binary



Path to teLeap executable used to build the system for AMBER


Returns the default leaprc forcefield files used by


Returns the default parameter frcmod files used by


Returns the default topology prepi files used by


Returns the location of the AMBER files distributed with HTMD


Lists all AMBER forcefield files available in HTMD


>>> from htmd.builder import amber
>>> amber.listFiles()             
---- Forcefield files list: ... ----