I found these words in the GROMACS v4.5.5 manual:

*[ atoms ] : defines the molecule, where nr and type are fixed, the rest is
user defined. So*
*atom can be named as you like, cgnr made larger or smaller (if possible,
the total charge of a **charge group should be zero), and charges can be
changed here too.*

So does it means the mass and charge of [ atomtypes ] section could be
modified in [ atoms ] section?

On 12 October 2016 at 23:30, Alan <alanwil...@gmail.com> wrote:

> But read the GMX manual to understand why it's all fine.
>
> On 12 October 2016 at 13:29, Dd H <ddhe...@gmail.com> wrote:
>
> > 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
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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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