VMD-L Mailing List

From: Tristan Croll (tristan.croll_at_qut.edu.au)
Date: Wed Feb 18 2015 - 19:54:09 CST

Just a note on the script Ashar linked to: "veclength [vecsub $vector1 $vector2]" is functionally equivalent to "vecdist $vector1 $vector2".

A minor thing, but it is nice to be efficient.

________________________________
From: owner-vmd-l_at_ks.uiuc.edu <owner-vmd-l_at_ks.uiuc.edu> on behalf of Ashar Malik <asharjm_at_gmail.com>
Sent: Thursday, 19 February 2015 9:08 AM
To: Jevgenij Raskatov; vmd-l_at_ks.uiuc.edu
Subject: Re: vmd-l:

you need to use the command "measure"

find it here:
http://www.ks.uiuc.edu/Research/vmd/vmd-1.9.1/ug/node136.html

you can do it by -- selecting 1 atom in aspartate and 1 atom in lysine and measuring the distance between them -- or calculating the centroid of aspartate and the centroid of lysine and calculating the distance between the centroids.

with "measure" you need to specify "bond" followed by the selections between which you want the distance to be calculated. For details read the "bond" section in the above link.

if you dont want to use measure you can make use of veclength --- the sample script for that would look something like this:

http://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/21073.html

hope this helps.

Best,
/A

On Thu, Feb 19, 2015 at 11:55 AM, Jevgenij Raskatov <jraskato_at_ucsc.edu<mailto:jraskato_at_ucsc.edu>> wrote:
Hi, I think it would be best to take a distance measure. Is there a way to specify this in vmd?

Thanks

On Wed, Feb 18, 2015 at 2:48 PM, Ashar Malik <asharjm_at_gmail.com<mailto:asharjm_at_gmail.com>> wrote:

Yes. What I can think of at the moment is that you can define two selections ( 1 being aspartate and other lysine) in each frame of your DCD measure the "specific contact" between them. If it satisfies a condition write out the selections or the specific thing you are measuring as a function of the frame number. To get more you might want to tell what the specific contact is? Is it a distance measure ? Or angle ?

On Feb 19, 2015 11:41 AM, "Jevgenij Raskatov" <jraskato_at_ucsc.edu<mailto:jraskato_at_ucsc.edu>> wrote:
Dear all,

I am analyzing an MD trajectory, trying to find structures that possess specific contacts between two amino acid side chains (i.e. aspartate and lysine). Is there a way to project a subset of structures to fulfill this criterion from a dcd-file?

Thanks

Jevgenij 

--
Dr. Jevgenij A. Raskatov
Assistant Professor in Chemistry and Biochemistry
Tel.: +1-831-459-2978<tel:%2B1-831-459-2978>
Department of Chemistry and Biochemistry
Physical Science Building 356
1156 High Street
Santa Cruz, CA
95064 USA
--
Dr. Jevgenij A. Raskatov
Assistant Professor in Chemistry and Biochemistry
Tel.: +1-831-459-2978<tel:%2B1-831-459-2978>
Department of Chemistry and Biochemistry
Physical Science Building 356
1156 High Street
Santa Cruz, CA
95064 USA
--
Best,
/A