[gmx-users] Mass and charge data are missing in [ atomtypes ] section.

[Alan]

It's all fine.

On 12 October 2016 at 12:34, Dd H <ddhecnu at gmail.com> wrote:

> 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 <alanwilter at 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 <ddhecnu at 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
> > United Kingdom
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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
United Kingdom
Tel: +44 (0)1223 494588