VMD-L Mailing List

From: Jordi Cohen (jordi_at_ks.uiuc.edu)
Date: Wed Jun 27 2007 - 11:29:31 CDT

Hi Rachel,

Implicit ligand sampling is included in the volmap command, but is
not present in the graphical user interface. For one, it requires
more parameters and data preparation than would easily fit in a GUI,
and the analysis of large trajectories can take a few days such that
it is more convenient to run VMD as a background process than using
the GUI. I have been preparing a set of utility scripts as well as a
binary for combining/altering the resulting maps, and you may find a
preliminary version of these here (a final version would be
distributed more officially on the TCBG website later). These may
help you get started:

    http://www.ks.uiuc.edu/~jordi/volmap/

As for AMBER vs CHARMM, that is not a problem. volmap simply needs to
know the Lennard-Jones parameters for each atom, of course. These are
supplied by putting the radius and energy parameters in CHARMM-form
into the radius and beta fields of VMD, as indicated. The supplied
script reads a CHARMM parameter file to extract these values and to
assign them to atoms. It would need to be modified somewhat to read
an AMBER param file and convert the parameters, as necessary. This
assignment is done before the actual implicit ligand analysis, so as
long as you fill in the radius/beta values of each atom, you could
use any force-field. Let me know if you need help with this, I have
to admit in advance I am not familiar with the AMBER format, so I
don't have any scripts ready for AMBER.

As for making nice pictures, this is an art :) Use a combination of
fog, orthographic mode, and clipping planes (or the front clipping
boundary). I've gotten quite good at this, so if you sent me a map, i
could probably send you a VMD state that would look good. However,
with a bit of practice, I'm sure you could achieve the same too...

This is a new method, so there is no completely ready-made fully
automatic way to analyze your trajectory just yet. You will need do
do some minimal scripting, and experimenting, etc. But hopefully, it
will be worth it.

Let me know if you need any additional assistance.

Cheers,
Jordi

On Jun 26, 2007, at 11:56 AM, Rachel wrote:

> Dear all,
>
> I have installed VMD1.8.6, as I read the documents about volmap, it
> supports ligand volmap which I am interested in. However, it is not
> in the volmap plugin?
>
> I read the paper by Cohen, J., A. Arkhipov, R. Braun and K.
> Schulten, "Imaging the migration pathways of CO, NO, and Xe or
> O ,inside myoglobin", Biophysical Journal 91, 1844-1857, 2006. What
> I want to do is look at the gas migration pathways inside a
> different protein which is similar to that paper. As the author
> used CHARMM force field in NAMD for the molecular dynamics, also in
> the volmap document it says "Before starting the computation, the
> atomic radii of each atom should be set to the corresponding CHARMM
> Lennard-Jones Rmin/2 parameter (in Angstroms), and the beta value
> of each atom should be set to the CHARMM Lennard-Jones epsilon
> (energy well depth in kcal/mol) parameter", however, the current
> package I am using is AMBER, can I ask is it possible to use the
> AMBER MD output to generate such ligand volmap in VMD? will there
> be any differences? And if it is compatible with AMBER results, can
> I ask are there any more detailed documents about using volmap and
> making corresponding nice pictures?
>
> Thank you all for any suggestions.
>
> Rachel