Thank you!

On 12 October 2016 at 19:50, Alan <alanwil...@gmail.com> wrote:

> It's all fine.
>
> On 12 October 2016 at 12:34, Dd H <ddhe...@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 <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
> > > 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
> --
> Gromacs Users mailing list
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