From: aneesh cna (aneeshcna_at_gmail.com)
Date: Thu Feb 25 2010 - 23:51:15 CST

Dear John,

              Thanks for your reply. I am sorry for making you confused
with my problem. My protein is inside a micelle and I want to put this
micelle inside the equilibrated box of organic solvent.

Thanks again for your reply

Sincerely
Aneesh

On Thu, Feb 25, 2010 at 5:33 PM, John Stone <johns_at_ks.uiuc.edu> wrote:

>
> 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/ <http://www.ks.uiuc.edu/%7Ejohns/>
> Fax: 217-244-6078
>