From: sajad falsafi (sajad.falsafi_at_yahoo.com)
Date: Sat Jun 04 2011 - 08:26:14 CDT

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-