It's unlikely that every dihedral plot would shoe something interesting and
relevant. Why don't you show just the ones that change during binding? You
also may consider showing data other than dihedral angles. Things like rmsd
are more global measures and dihedral angles are very local.
On Jun 22, 2016 1:18 AM, "Sehrish Naz Aijaz" <sehrish.naz.outlook.com>
wrote:
> Dear All,
> I have run protein-protein simulation to investigate the conformational
> changes in protein after binding with its ligand protein. I have plotted
> the graphs of dihedral angles using Cpptraj tool in amber. Though I can
> present my results in the graphical form but the number of graphs would be
> needed for that which will exhaust the reader. Therefore, I want to know is
> there a better tool to present the cumulative data on dihedral angles in
> either a tabulated or graphical form.
>
> Regards,
>
> Sehrish Naz
>
> Jr. Research Fellow,
> Computational Chemistry Unit.
> Dr. Panjwani Center for Molecular Medicine and Drug Research,
> International Center for Chemical and Biological Sciences,
> University of Karachi, Karachi-75270.
> E-mail: Sehrish.naz.outlook.com
>
> From: David A Case<mailto:david.case.rutgers.edu>
> Sent: 21 June 2016 22:25
> To: AMBER Mailing List<mailto:amber.ambermd.org>
> Subject: Re: [AMBER] Problem analysing output with process_mdout.perl
> script
>
> On Tue, Jun 21, 2016, Ruth Helena Tichauer wrote:
> >
> > When analysing my output files with the script “process_mdout.perl”, I
> > find that it is not retrieving the density, nor the volume, of my system
> > as both summary.DENSITY and summary.VOLUME files only contain the time
> > elapsed. Am I using an “old” version? You can find it in attachements.
>
> First, try process_mdout.perl on a sample mdout file like this one:
> $AMBERHOME/test/ubiquitin/mdout.ubiquitin.save.
>
> Second, as a sanity check, make sure you actually have Density and VOLUME
> lines in your mdout file.
>
> ...good luck...dac
>
>
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Received on Wed Jun 22 2016 - 03:30:02 PDT
