VMD-L Mailing List

From: Dennis N Bromley (dbromley_at_uw.edu)
Date: Sat Jun 04 2011 - 12:14:40 CDT

Hi Sajad,

Thanks for the tip! I currently have two pdb files - actually one pdb file
with the receptor and one pdbqt file from AutoDock Vina with multiple ligand
poses in it. If I assume that I'm taking the best pose, I could reduce that
to one and then combine the best pose with the receptor into a single PDB.

Is there a simple way to handle the twp pdb file setup like I have? Or is
combining them together the best way to go?

thanks!
-denny-

On Sat, Jun 4, 2011 at 6:26 AM, sajad falsafi <sajad.falsafi_at_yahoo.com>wrote:

> Hi denny,
>
> Please let me know that you have two PDB files or only one PDB.
> if you have only one PDB file, you should type :
> "chain X and same residue as within 5 of chain Y"
> (istead of chain X you should type chain of receptor and istead of chain Y
> type chain of ligand)
> also for better analysis you can merge two of the PDB files into single
> PDB.
>
>
> hope this helps you
> Sajad
>
> ------------------------------
> *From:* Dennis N Bromley <dbromley_at_uw.edu>
> *To:* vmd-l_at_ks.uiuc.edu
> *Sent:* Sat, June 4, 2011 7:57:58 AM
> *Subject:* vmd-l: how do I show contacts with XXX angstroms between a
> protein and a ligand?
>
> Hi everyone,
>
> I'm sorry if this is a common newbie question - I've looked everywhere
> including the mailing list archives. Someone did ask this question a while
> ago but the response was "have you tried 'within'?" which pointed me in the
> right direction but alas, I'm still having problems.
>
> Anyway, if someone could help me with the syntax I would be forever
> grateful. I have a protein call 'receptor' and a small molecule called
> 'ligand' and I'm trying to show the protein side chains that interact with
> the ligand atoms. In spirit I want to write "same residue as within 5 of
> (molname 'ligand)'" but I can't seem to figure out exactly how to put the
> syntax together.
>
> Again, sorry if this has been answered somewhere and I just missed it.
>
> thanks!
> -denny-
>
>
>
>
>