VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Wed Oct 21 2009 - 13:03:57 CDT

On Wed, Oct 21, 2009 at 12:56 PM, Umesh Ghoshdastider
<fraternitydisposal_at_gmail.com> wrote:
> Hi there,

hi umesh,

> I recently started using vmd and having hard time solving following problems:
>
> 1. How can I align or superimpose two CG protein structures? I can't
> do it in other software since it is CG and I had to write a script so
> that vmd connects and colors the grains of the protein which other
> softwares don't understand. Just manually moving molecules by mouse
> does not work.

please note, that VMD has no concept at all of what kind of molecule
you actually have in your systems. there are only a few convenience
methods, that heavily rely on conventions that are common in certain
all-atom force fields. however, that only means, that some scripts based
on those conventions will fail, if you change them to use whatever
conventions you use, or write your own scripts/modules/plugins then
they will work just fine. the alignment module just takes a bunch of
atoms as input and computes a transformation matrix.

> 2. How can I count no. of other molecules (say resname abc) around the
> given distance from the protein over time? Is it possible to color
> those molecules, given the distance from the protein?

there are many ways to do this and it is difficult to give other general
advice than, learn vmd script writing from the existing VMD (and Tcl!)
tutorials and build a script that does this step by step. there are scripts
that do similar things, and there are repeated discussions on the subject
on this list. please check the archive and script library for useful components.
but ultimately you will have to write a script for your specific needs.

cheers,
   axel.

>
> Thanks a lot for your trouble.
>
> Best regards,
> Umesh
> 

-- 
Dr. Axel Kohlmeyer    akohlmey_at_gmail.com
Institute for Computational Molecular Science
College of Science and Technology
Temple University, Philadelphia PA, USA.