The ACPYPE Portal was designed to
generate topology parameters files for unusual organic chemical compounds. It is based on
and so far, ACPYPE is
able to work for CNS/XPLOR, GROMACS, CHARMM and AMBER.
The main scope for ACPYPE Server is to help to pave the way for
automatic molecular dynamics simulations involving molecules with unknown parameters,
like for example, in complexes of protein and inhibitor, where the ligand is usually
an unusual chemical compound.
ACPYPE stands for AnteChamber PYthon Parser
interfacE and is pronounced "ace + pipe".
If you use this resource, please cite:
If you use non-uniform 1-4 scale factor conversion (e.g. if using GLYCAM06), please cite:
This service is provided with ABSOLUTELY NO WARRANTY and holds no liabilities. If you decide to
use it, bear in mind that your data and potential results are not stored with encryption,
and the service administration has access to it. Furthermore, the data and results will be
eventually removed after two weeks from the time of submission, whether your job has finished or not.
This is the beta version of the ACPYPE webserver and is not production stable.
However, please feel free to use it and report any bugs or strange behaviour to the
What the ACPYPE Server does
It will take a PDB, MDL or MOL2 file of a small organic molecule without open valence and
assign charges and force ﬁeld parameterizations according to GAFF (Generalised Amber Force Field).
There are some options that can be applied to a submitting project.
For charge, there are three methods:
For net charge
- bcc: for semi-epirical AM1-BCC, parameterized to reproduce HF/6-
31G* RESP charges; slow, but with good cost/benefit (default)
- Gasteiger method, very fast but less accurate
- user: for a MOL2 file with charges already calculated, via, e.g.,
, set a integer value for the project, or let ACPYPE guess
the net charge for the molecule.
For atom type, set GAFF (default), GAFF2 or AMBER. If set AMBER, ACPYPE/antechamber
will try to set parameters and atom types according to AMBER14SB forcefield. Case
it fails, GAFF parameters (but with AMBER atom types) will be used.
What the ACPYPE Server doesn't do
It will not work with organic molecule with open valences; containing others atoms
than C, N, O, S, P, H, F, Cl, Br and I; or covalently
bonded to another molecule. If one wants parameters for a modified amino acid
residue, one way of getting it is by neutralising the N- and C- termini and then fit
manually the additional parameters to the modified residue.
How ACPYPE web interface works
The web interface was designed to be simplest way to obtain topologies parameters
for small molecules from a coordinate file, by intuitive steps. The steps are:
- Upload a PDB, MDL or MOL2 file
- Select options and submit
- Follow the job status
- Retrieve results when job finished
The scheme here depicts the workflow of ACPYPE server.
Documentation and help
More information, with references, can be found at
More help? Don't hesitate: Administrator