[gmx-users] GBSA with ligands

Alan alanwilter at gmail.com
Fri Oct 12 14:24:02 CEST 2012

Hi, the issue is not with Antechamber or Acpype. There were similar
questions to yours here (try searching GMX mail archives). The problem is
you need to create the GBSA.itp parameters for you ligand.

Which Acpype does is to create/convert Amber/GAFF parameters to usual MD in


On 12 October 2012 11:34, Leandro Bortot <leandro.obt at gmail.com> wrote:

> Dear users,
>      After parametrizing a ligand with antechamber and converting the
> topology and structure files with acpype I can't do GBSA simulations in
> GROMACS because of missing GB parameters. In fact, the implicit solvent
> parameters weren't converted from the AMBER topology (.prmtop) to the
> GROMACS topology (.top) by acpype.
>      There is a "FLAG RADII" in the .prmtop but there is no [
> implicit_genborn_params ] in the .top.
>      Is this an issue with acpype?
>      Any help would be greatly appreciated
> Best regards,
> Leandro
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Alan Wilter SOUSA da SILVA, DSc
Bioinformatician, UniProt - PANDA, EMBL-EBI
CB10 1SD, Hinxton, Cambridge, UK
+44 1223 49 4588

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