Webserver update on 2023-01-24: New version of ACPYPE is now available
We are pleased to announce that our webserver has been updated with the latest version of our service.
We apologize for any inconvenience this may have caused and thank you for your patience during this process.
If you have any questions or concerns, please do not hesitate to contact the ACPYPE Server development team.
About
The ACPYPE Portal was designed to generate topology parameters files for unusual organic chemical compounds. It is based on ANTECHAMBER 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:
- SOUSA DA SILVA, A. W. & VRANKEN, W. F. ACPYPE - AnteChamber PYthon Parser interfacE. BMC Research Notes 2012, 5:367
- KAGAMI, L. P., SOUSA DA SILVA, A. W., DÍAZ, A., & VRANKEN, W. F., The ACPYPE web server for small-molecule MD topology generation, Bioinformatics, Volume 39, Issue 6, June 2023, btad350
If you use non-uniform 1-4 scale factor conversion (e.g. if using GLYCAM06), please cite:
Disclaimer
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.What the ACPYPE Server does
It will take either a SMILES input or files in format PDB, MDL or MOL2 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:
- 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., R.E.D.-III
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
Documentation and help
More information, with references, can be found at ACPYPE GitHub pages.More help? Don't hesitate to contact to: the Website administrator
