[gmx-users] Issue with the PDB generated after topology

[Mark Abraham]

Hi,

On Mon, Jul 3, 2017 at 11:34 AM Khadija Amine <kh.amine1 at gmail.com> wrote:

> Hi Mark,
>
> Is there any way to renumber my protein sequence at the end of the
> simulation?
>

Sure gmx editconf -resnr, as Joao suggested is good.

But you aren't going to get a sensible plot if residues in different chains
within the same structure have the same numerical identifier within the
analysis. You're either going to have to do separate analyses for each
chain (perhaps with -resnr), or rely on differently labelling your axes.

Mark


> The numbering is very important in RMSF plot for example.
>
> Thank you
>
> *Khadija Amine*
> Ph.D. Biology and Health
> Biochemistry & Bioinformatics
> Phone: 33339584
> --
> 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-request at gromacs.org.
>