From: John Stone (
Date: Thu Feb 25 2010 - 16:33:13 CST

  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.

  John Stone

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

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