VMD-L Mailing List

From: sajad falsafi (sajad.falsafi_at_yahoo.com)
Date: Tue Jun 07 2011 - 04:55:18 CDT

Hi,

We suggest to use edit in Text Editor , it is more simple than this way. because
your way need topology or PSF files.

hope this helps you
Sajad and Zahra

________________________________
From: John Stone <johns_at_ks.uiuc.edu>
To: Dennis N Bromley <dbromley_at_uw.edu>
Cc: sajad falsafi <sajad.falsafi_at_yahoo.com>; vmd-l ks.uiuc.edu
<vmd-l_at_ks.uiuc.edu>
Sent: Mon, June 6, 2011 11:12:29 PM
Subject: Re: vmd-l: how do I show contacts with XXX angstroms between a protein
and a ligand?

Hi,
  You can use one of the plugins (Extensions->Modeling->Merge Structures),
one of the structure building tools (e.g. topotools, psfgen), or one of the
VMD example scripts (see "mergepdbs") to do this all within in VMD.
If you use the low level structure building tools you have complete control
over chain assignment and such. I don't recall off the top of my head what
the default behavior of the automated scripts/plugins is in that regard.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Sat, Jun 04, 2011 at 10:27:05AM -0700, Dennis N Bromley 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-
>
> 

-- 
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