Welcome to ACPYPE’s documentation!
ACPYPE - AnteChamber PYthon Parser interfacE
A tool based in Python to use Antechamber to generate topologies for chemical compounds and to interface with others python applications like CCPN and ARIA. Topologies files to be generated so far: CNS/XPLOR, GROMACS, CHARMM and AMBER.
Quick start
acpype has two modes, and both are a single command.
From a small molecule – a .mol2, .pdb, .mdl/.mol file, or a SMILES
string – it drives the whole AmberTools pipeline:
acpype -i molecule.mol2 -b MOL -c bcc -n 0 -a gaff2
That single command does the work of three separate AmberTools runs – antechamber
to assign atom types and charges, parmchk2 to fill in missing parameters, and
tleap to build the topology – and then also writes GROMACS, CNS/XPLOR and CHARMM
versions into one MOL.acpype/ folder.
From existing AMBER files, converting a LEaP prmtop/inpcrd pair to GROMACS
without needing AmberTools at all:
acpype -p FFF_AC.prmtop -x FFF_AC.inpcrd
Run acpype -h for every option and a description of each output file. The
README covers installation and
worked examples for GROMACS, CNS/XPLOR and NAMD.
Using ACPYPE as a library
acpype.acs_api.acpype_api returns the generated topologies as a JSON string, and
acpype.topol.ACTopol exposes the same pipeline as an object:
from acpype.topol import ACTopol
molecule = ACTopol("molecule.mol2", chargeType="bcc", atomType="gaff2", basename="MOL")
molecule.createACTopol()
molecule.createMolTopol()
The full API is documented below.
API reference
The Package |