atomselect option for extracting protein-ligand complex

From: KK R (
Date: Mon Feb 17 2014 - 16:16:43 CST


I am trying to select a set comprising 'protein', 'ligand' and 'water
residue within 10 angstroms of the ligand LIG' in the VMD console to write
them into PDB file from dcd trajectory. I tried to do it using the
following atomselect command:

set sel [atomselect top "{protein} and {resname LIG} and {water within 10
of (resname LIG)}"]

My ultimate purpose is to extract "complex of protein-ligand and waters
residing within 10A of ligand" from DCD trajectory. The whole script, I am
using, is given below:
set sel [atomselect top "{protein} and {resname LIG} and {water within 10
of (resname LIG)}"]
set n [molinfo top get numframes]
set outname "protligwater_"
for { set i 0 } { $i < $n } { incr i } {
 $sel frame $i
 $sel update
 set name [format "%s%.9d.pdb" $outname $i]
 $sel writepdb $name
It successfully writes pdb files, but all are empty as nothing was selected
from the atomselect command.
Any suggestion on it will be highly appreciable.

Best regards,

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