VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Mar 03 2009 - 14:51:18 CST

Hi,
  I'd suggest using MSMS for your surface representation, as it gives
nice looking surfaces. You can draw springs and other graphical objects
using the "draw" or "graphics" commands in VMD. There are various example
scripts for drawing arrows etc in the VMD/CPMD tutorial here:
  http://www.theochem.ruhr-uni-bochum.de/~axel.kohlmeyer/cpmd-vmd/part7.html#chap9_sect1

There's an old spring drawing script here:
  http://www.ks.uiuc.edu/Research/vmd/script_library/scripts/spring/

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Sun, Mar 01, 2009 at 03:23:12PM -0600, Falgun Shah wrote:
> Dear Vmd users
>
> I am doing constant velocity smd simulation of the protein of my interest. I
> want to generate final image of the protein in surface representation along
> with virtual spring showing 3 direction of egress for my ligand. Please let
> me know the best way to generate molecular surface of protein binding site
> and how to insert spring between COM of the smd atoms and the calculated
> direction. Your recommendations are most welcome. Thanks in advance.
> --
> Falgun H shah
> PhD candidate (3rd year)
> Department of Medicinal Chemistry
> 2028, Natural Product Center
> University of Mississippi
>
> Ph No: 6629151286(O)
> 662 801 5667(M)
> email: fhshah_at_olemiss.edu 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349
  WWW: http://www.ks.uiuc.edu/~johns/      Fax: 217-244-6078