VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_cmm.chem.upenn.edu)
Date: Wed Jan 23 2008 - 03:49:49 CST

On 1/23/08, Francesco Pietra <chiendarret_at_yahoo.com> wrote:
> Could you please direct me to a tcl script suitable to detect (and list) the
> protein residues at a distance of choice from a single-residue organic ligand?
> I would like to follow that course in parallel to the rmsd course of protein
> and ligand during the MS. The protein-ligand are embedded in a POPC membrane,
> TIP3P solvated.
>
> It would also be helpful if the script allows to select specific atoms of the
> ligand and determine their proximity to the protein residues (or atoms of
> these).

ciao francesco,

...and i would like to have a tcl script that writes grant proposals
and if possible, successful ones. ;-)

if you want anything this specific and flexible, you're most likely stuck
writing it yourself. there is a remote chance somebody has written
something similar and you can adapt it.

...and then, of course, there is the problem, that (too?) many people don't
submit their scripts or script fragments to the VMD script library, so a lot
of useful stuff is lost when they move on to other projects.

other than that, there is also the alternative of sponsoring somebody
with the proper expertise to write a custom script. since people spend
a lot of money on computers and (commercial) software, i am always
wondering why there is nobody offering 'incentives' to get their specific
problem solved (by and expert and quickly).

i'd be very interested to learn how people here on this mailing list
see the perspective of having their technical problems sort of
'contracted out' so they can focus on the science...

cheers,
     axel.

>
> In doing that from prmtop/mdcrd (I am working with Amber in this moment) I
> guess that atoms names should be read from a pbd generated from prmtop/mdcrd,
> and given to the script in their precise format (I mean, for example, that atom
> names in ff99SB for the protein are uppercase, while those for the ligand in
> GAFF ff are lowercase).
>
> That applies also to Luis Gracia's RMSD Traj Tool that I am finding extremely
> useful and time saving.
>
> Thanks
> francesco pietra
>
>
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-- 
=======================================================================
Axel Kohlmeyer   akohlmey_at_cmm.chem.upenn.edu   http://www.cmm.upenn.edu
  Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
=======================================================================
If you make something idiot-proof, the universe creates a better idiot.