mohammad.r0325 at yahoo.com
Mon Dec 12 07:05:36 CET 2016
I used these commands for installing:
sudo wget ftp://ftp.cmbi.ru.nl/pub/software/dssp/dssp-2.0.4-linux-amd64 -O /usr/local/bin/dssp
sudo add-apt-repository ppa:sfleischmann/tcbsys
sudo apt-get update
sudo apt-get install dssp
and these for running:
do_dssp -f md.xtc -s md.tpr -o dsso.xpm -sc dssp.xvg
xpm2ps -f dssp.xpm -o dssp.eps -di ps.m2p
ps2pdf dssp.eps dssp.pdf
From: Amir Zeb <zebamir85 at gmail.com>
To: gmx-users at gromacs.org
Sent: Monday, 12 December 2016, 6:05:23
Subject: Re: [gmx-users] Analaysis
can you please let me know how to install do_dssp on my gromacs 5.0.6
we have downloaded the package but we could not install
On Dec 11, 2016 11:45 PM, "Justin Lemkul" <jalemkul at vt.edu> wrote:
> On 12/11/16 1:01 AM, Mohammad Roostaie wrote:
>> Hi Gromacs users, I want to obtain the percentage of helicity of a peptide
>> with respect to time after the simulation, how can I get it? I used the
>> helix" and "gmx do_dssp" commands, but I could not get it. In addition, I
> The last line in scount.xvg from gmx do_dssp gives you this.
> want to get the number of clusters and contact area of two particles with
>> respect to time, and I used "gmx clustsize" and "gmx mindist" commands,
>> but I
>> still cannot get these factors. can you please help me figure this out?
> gmx clustsize has output options for number of clusters, cluster size,
> distribution, etc.
> If you want contact area, use gmx sasa with appropriate index groups.
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> Gromacs Users mailing list
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