Dear Mathias,
In the old days, I used a program called "ligplot", which gives you
a .ps output file with the interactions involved, and the distances.
I'm using PyMol as well, but things might not be exactly what you
want. Here, I'm just looking at residues 4.2 angstrom away in the
interacting pocket between my protein and my ligand. It's very fast
to do, and you can even have an output picture. Following is a fast
script where protein.pdb and ligand.pdb are the required files.
Please note that in addition to the picture generated, the script
will also generate two files with interacting residues in one, and
interacting atoms in the other. Again, I'm not sure that it will be
of any use still...
#####Run this under PyMol#####
delete all
## settings for the final picture ##
set depth_cue=1
set ray_trace_fog=1
set cartoon_discrete_colors, 1
set dot_solvent, 1
set dot_density, 3
set dot_color, white
space cmyk
set sphere_scale, 0.25
## load your 2 pdbs ##
load protein.pdb, my protein
load ligand.pdb, my_ligand
## look at the interacting residues ##
h_add
flag ignore, none
from pymol import cmd
ligand_area=cmd.get_area("my_ligand")
protein_area=cmd.get_area("my_protein")
create my_complex, my_ligand|my_protein
complex_area=cmd.get_area("my_complex")
from pymol import stored
## interacting residues set at 4.2 angstrom distance ##
cmd.select("interacting_atoms", "* w. 4.2 of my_ligand")
stored.list=[]
cmd.iterate("interacting_atoms", "stored.list.append((resi, resn))")
select interacting_residues, br. interacting_atoms
disable interacting_residues
## generate the picture ##
color white, my_protein
color yellow, my_ligand
color blue, e. n
color red, e. o
color forest, e. s
color orange, e. p
hide
show spheres, interacting_atoms&!e. h
show sticks, interacting_residues&!e. h
label (name ca+C1*+C1'&(br.(interacting_residues))),"%s-%s"%(resn,resi)
save interacting_residues.pdb, interacting_residues, quiet=0
save interacting_atoms.pdb, interacting_atoms, quiet=0
orient
zoom interacting_residues
## numerical values of surface interactions ##
print ligand_area
print protein_area
print complex_area
print (ligand_area + protein_area) - complex_area
#####
All the best.
Leo
On Feb 28, 2007, at 3:43 AM, mathias wrote:
Dear all,
Can anyone of you guys recommend free software, or any open access
internet server, to calculate VDW interactions of small molecules
binding to protein. The only information I need is an output file
which lists all amino acids of the target protein which make VDW
interactions with the binding small molecule.
Thank you very much for your help and recommendations,
Mathias
==========================
Chavas Leonard M.G., Ph.D.
Structural Research Center
KEK,PF. 1-1 Oho
Tuskuba, Ibaraki - Japan
---------------------------------------------
PHS: +81(0)29-864-5200 (ext: 2682)
e-mail: [EMAIL PROTECTED]
URL: http://pfweis.kek.jp/~leo
==========================
