[gmx-users] MD simulations of two chains protein

[Mark Abraham]

Hi,

It's hard for anyone to know what you're doing and seeing unless you share
actual command lines, and upload your resulting graphs to a file-sharing
service and provide a link (the list does not take attachments)

Mark

On Tue, 15 Nov 2016 08:51 Khadija Amine <kh.amine1 at gmail.com> wrote:

> Ok I will try that.
>
> There is a way to specify the regions to plot in RMSF using rms tool?
>
> Thank you
>
> *Khadija AMINE*
>
>
> *Computational Biology*
> *Postdoctoral Research Associate*
> *Carnegie Mellon University*
>
> On Tue, Nov 15, 2016 at 10:40 AM, Khadija Amine <kh.amine1 at gmail.com>
> wrote:
>
> > Hello,
> >
> > Can someone show me how can I proceed?
> >
> > Thank you
> >
> > *Khadija AMINE*
> >
> >
> > *Computational Biology*
> > *Postdoctoral Research Associate*
> > *Carnegie Mellon University*
> >
> > On Mon, Nov 14, 2016 at 2:33 PM, Khadija Amine <kh.amine1 at gmail.com>
> > wrote:
> >
> >> Dear Gromacs users,
> >>
> >> I need your help regarding MD simulation of two chains protein.
> >> The chain A is 2-78 aa, and the chain B is 1-168 aa.
> >>
> >> I started with the pdb file where there is specified names of the two
> >> chains as A and B.
> >>
> >> I did solvation of my system in a cubic box, I tried to open the
> >> pdb file issued from this step I didn't find the column specifying the
> >> chain names.
> >>
> >> I run 20 ns of MD for this protein. The RMSF plot of the protein seems
> >> to be overlapping from 1 to 78 and the rest of the residues flctuation
> >> is good.
> >>
> >> As it is the first time am facing such issues with protein with two
> >> chains, how can I avoid such overlap in RMSF plot?
> >>
> >> Is this linked to the chains numbering issued after writing the
> topology.
> >>
> >> Thank you
> >>
> >> *Khadija AMINE*
> >>
> >>
> >> *Computational Biology*
> >> *Postdoctoral Research Associate*
> >> *Carnegie Mellon University*
> >>
> >
> >
> --
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