I use this command:
acpype -p filename.prmtop -x filename.inpcrd

It generates parameter files for GROMACS and my question is about the .top
file of outputs.

On 12 October 2016 at 18:22, Alan <alanwil...@gmail.com> wrote:

> Which acpype command did you specifically used?
>
> acpype may be able to use Antechamber and calculate partial charges. See
> acpype -h
>
> On 12 October 2016 at 09:56, Dd H <ddhe...@gmail.com> wrote:
>
> > Hi everyone,
> > I generated a .top file of a ligand using acpype for MD simulations.
> There
> > are some new atom types in [ atomtypes ] section, but the data of mass
> and
> > charge columns of the section are zeros. However they can be found in
> the [
> > atoms ] section. Can you tell me if this file is ok for MD simulations?
> > Thank you in advance!
> >
> > Dading Huang
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>
> --
> Alan Wilter SOUSA da SILVA, DSc
> Senior Bioinformatician, UniProt
> European Bioinformatics Institute (EMBL-EBI)
> European Molecular Biology Laboratory
> Wellcome Trust Genome Campus
> Hinxton
> Cambridge CB10 1SD
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