VMD-L Mailing List

From: Francesco Pietra (chiendarret_at_yahoo.com)
Date: Wed Jan 23 2008 - 01:40:51 CST

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).

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

      ____________________________________________________________________________________
Looking for last minute shopping deals?
Find them fast with Yahoo! Search. http://tools.search.yahoo.com/newsearch/category.php?category=shopping