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 > > > > > -- > > > > > Gromacs Users mailing list > > > > > > > > > > * Please search the archive at http://www.gromacs.org/ > > > > > Support/Mailing_Lists/GMX-Users_List before posting! > > > > > > > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > > > > > > > * For (un)subscribe requests visit > > > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users > > or > > > > > send a mail to gmx-users-requ...@gromacs.org. > > > > > > > > > > > > > > > > > > > > > -- > > > > 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 > > > > > > > > * Please search the archive at http://www.gromacs.org/ > > > > Support/Mailing_Lists/GMX-Users_List before posting! > > > > > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > > > > > * For (un)subscribe requests visit > > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users > or > > > > send a mail to gmx-users-requ...@gromacs.org. > > > > > > > -- > > > Gromacs Users mailing list > > > > > > * Please search the archive at http://www.gromacs.org/ > > > Support/Mailing_Lists/GMX-Users_List before posting! > > > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > > > * For (un)subscribe requests visit > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > > send a mail to gmx-users-requ...@gromacs.org. > > > > > > > > > > > -- > > 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 > > > > * Please search the archive at http://www.gromacs.org/ > > Support/Mailing_Lists/GMX-Users_List before posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe requests visit > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > send a mail to gmx-users-requ...@gromacs.org. > > > -- > Gromacs Users mailing list > > * Please search the archive at http://www.gromacs.org/ > Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- 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 * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.