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 Tue Jun 21 2016 - 22:30:02 PDT
