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

[Alan]

But read the GMX manual to understand why it's all fine.

On 12 October 2016 at 13:29, Dd H <ddhecnu at gmail.com> wrote:

> Thank you!
>
> On 12 October 2016 at 19:50, Alan <alanwilter at gmail.com> wrote:
>
> > 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
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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