[gmx-users] Analaysis

[‪Mohammad Roostaie‬ ‪]

Hi Amir,
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


Best,Mohammad
      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
   
hello mohammad

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
please help

thanks

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
>> "gmx
>> 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?
>> Thank
>>
>
> 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
>
> --
> ==================================================
>
> 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
> http://mackerell.umaryland.edu/~jalemkul
>
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