VMD-L Mailing List

From: Dennis N Bromley (dbromley_at_uw.edu)
Date: Sat Jun 04 2011 - 12:27:05 CDT

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-
>>
>>
>>
>>
>>
>
>