VMD-L Mailing List

From: sajad falsafi (sajad.falsafi_at_yahoo.com)
Date: Sun Jun 05 2011 - 08:06:56 CDT

Hi denny,

I'm sorry for replying late
The best way to combining them together is Copy and Paste both of them in Text
editor.
you can do the following :
Take the protein pdb and add a TER card on the end. The cat the receptor pdb
file onto the end of the protein one.
I don't know details of your pdb files
would you please send me pdb files to help you better.

hope this helps you
Sajad

----- Forwarded Message ----
From: Dennis N Bromley <dbromley_at_uw.edu>
To: vmd-l ks.uiuc.edu <vmd-l_at_ks.uiuc.edu>
Sent: Sun, June 5, 2011 6:54:26 AM
Subject: Re: vmd-l: how do I show contacts with XXX angstroms between a protein
and a ligand?

ok, another newbie question.

I can *see* all the residues now, but how do I get VMD to tell me which residues
I'm actually looking at? I'm figuring it must be some command line thing along
the lines of

resid of (my command from below)

thanks!
-denny-

On Sat, Jun 4, 2011 at 11:09 AM, Dennis N Bromley <dbromley_at_uw.edu> wrote:

in case anyone is searching the archives later, here is an update for finding
hydrophobic contacts.
>
>same residue as ((name "C.*") and index > 30 and within 5.4 of (index < 31 and
>name "C.*") )
>
>again, however, more elegant solutions are always invited. :)
>
>-denny-
>
>
>
>
>On Sat, Jun 4, 2011 at 10:27 AM, Dennis N Bromley <dbromley_at_uw.edu> wrote:
>
>not hugely elegant, but I think this will work.
>>
>>Pymol combined both structures into a single pdb for me but put my ligand as
>>atoms 1-31 and the protein atoms as 32 ->. So, no chains. However, I did find
>>that this worked:
>>
>>same residue as (within 5.4 of (index 0 to 30))
>>
>>Again, a little klugey. But it will make the figure. :)
>>
>>Any advice for a more elegant solution that doesn't involve trolling through the
>>pdb file in notepad to discover atoms numbers would be much appreciated. :)
>>
>>-denny-
>>
>>
>>
>>
>>
>>
>>
>>On Sat, Jun 4, 2011 at 10:14 AM, Dennis N Bromley <dbromley_at_uw.edu> wrote:
>>
>>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-
>>>>
>>>>
>>>>
>>>>
>>>>
>>>
>>
>