VMD-L Mailing List

From: Ashar Malik (asharjm_at_gmail.com)
Date: Wed Feb 18 2015 - 16:48:31 CST

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> 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
>
> Department of Chemistry and Biochemistry
> Physical Science Building 356
> 1156 High Street
> Santa Cruz, CA
> 95064 USA
>