From: KK R (kkres14_at_gmail.com)
Date: Mon Feb 17 2014 - 16:16:43 CST
Hi,
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,
Roy
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