VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Feb 25 2010 - 16:33:13 CST

Hi,
  I think that what you really want to do is to merge your two structures
into one, and then use an atom selection to cut the hole with
"not within XXX of protein" and then write out the new structure.
This ought to work much better than attempting to dock your protein
into a hole that you cut independently.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Wed, Feb 24, 2010 at 02:04:27AM -0500, aneesh cna wrote:
> Dear VMD users,
> My simulation system is a well equilibrated cubic box
> of organic molecules. Now I want to put the protein inside this solvent
> box. For this first I tried to make a hole in the center of the box using
> the command ' all and (not within 30 of resid 1) ' ( residue 1 is almost
> in the center of the box) and and it worked fine. Then I load protein
> molecule and tried move it towards the the hole ( just by using mouse and
> looking at OpenGL display), but I cant able to make it out successfully.
> Is there any other way to approach this problem?. Waiting for your
> valuable reply
>
> Thanks in Advance
>
> Sincerely
> Aneesh 

-- 
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