AMBER Archive (2009)

Subject: Re: [AMBER] RMSD vs time and RMSD vs residues

From: Luis Gracia (lug2002_at_med.cornell.edu)
Date: Fri Oct 02 2009 - 13:07:10 CDT

Hi,

I wrote a program for this kind of problems long time ago. I haven't updated
for some time, but it might still work with the new Amber format.
http://sourceforge.net/projects/plotamber/

Luis 

--
Luis Gracia, PhD
Scientific Software Specialist
Department of Physiology & Biophysics
Weill Cornell Medical College
1300 York Avenue, Rm LC-501F
New York, NY 10065

Tel: (212) 746-6375
Fax: (212) 746-6226
lug2002_at_med.cornell.edu

On Fri, Oct 2, 2009 at 1:40 PM, Olotu Odunayo <paxoo_at_nottingham.ac.uk>wrote:

>
>
>
> Hi I was wondering if anyone knows how to calculate RMSD vs time in AMBER
> 10, if you have written your trajectory files (ntwx) in number of different
> steps e.g
> ntwx=50 and
> ntwx=100
>
> I have used
> trajin xx.mdcrd 1 2
> trajin dd.mdcrd
> rms first mass out filename.rms :1-270
>
> i get an output, but then the time scale on x-axis didn't come out right?
>
> Two,
>
> has anyone got a sample script on how i can calculate RMSD, to find out how
> much particular residues have moved.
> thanks
>
>
>
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