VMD-L Mailing List

From: Esteban Gabriel Vega Hissi (egvega_at_gmail.com)
Date: Wed Aug 12 2009 - 16:07:37 CDT

Hi,
Why don't you try to place your compound in the protein pocked using a
docking software, restraining any dihedral angle in the compound (rigid
mode). Try Autodock Vina.

Hope this help.

Esteban
UNSL

2009/8/12 Steve Seibold <seibold_at_chemistry.msu.edu>

> Hello
> Thanks for the response.
> I am using the mouse. Basically I toggle "F" in the "VMD Main" menu and
> freeze one molecule and move the other with respect to the first using
> "translate, rotate". I guess this is not really moving the pdb coordinates.
> I am not sure how else to do it. I don't know how do use the "move" mode
> using the mouse or the move/moveby in the TKconsole. Is there a tutorial
> that would show me these tools? I looked on-line but could not find anything
> pertinent. Did I miss it? Can you direct me to it if it exist. I would be
> happy to learn by trial and error in the tutorial.
>
> Thanks, Steve
>
> -----Original Message-----
> From: John Stone [mailto:johns_at_ks.uiuc.edu]
> Sent: Wednesday, August 12, 2009 3:59 PM
> To: Steve Seibold
> Cc: vmd-l_at_ks.uiuc.edu
> Subject: Re: vmd-l: positioning of a compound
>
>
> Hi,
> Are you moving the atom coordinates manually using the
> Mouse->Move->Molecule menu, or are you using atom selections for this
> purpose?
>
> Cheers,
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Wed, Aug 12, 2009 at 03:48:23PM -0400, Steve Seibold wrote:
> > I have constructed a pdb model of a compound and am trying to place it
> in
> > my protein. When I do this I open up both protein pdb and my compound
> pdb
> > simultaneous in VMD. The problem is when I try to position the
> compound
> > into the pocket of the protein. I cannot seem to move it closer in the
> > sense that no matter how long I freeze the protein and move the
> compound
> > it never appears to get closer. Is this just because it is VERY
> difficult
> > or is there some barrier to doing this. I attempted it for quite some
> time
> > and could never get the compound positioned correctly. Is there a way
> to
> > do this with VMD. I am using the WINDOW version.
> >
> >
> >
> > Thanks, Steve
> >
> >
> >
> >
> >
> >
>
> --
> 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
>
>