VMD-L Mailing List

From: Nupur Bansal (nupur.b298_at_gmail.com)
Date: Mon Oct 07 2013 - 15:28:04 CDT

Hi,

I have a protein-ligand complex simulated using Amber. Now, I am trying to find the residues closest to the ligand using VMD. The script is giving me an error "No timestep available for 'within' search! " and is selecting all the residues of the protein.
I don't know why this is happening. Can somebody help me in debugging this error?

This is the script that I am using:

set first 0
set last 0

set sys [mol new cur1_sb_strip.prmtop]
mol addfile type <netcdf> cur1_sb_strip.netcdf first$first last$last waitfor all

set all [atomselect $sys all]
for {set k 0} {$k <= $last} {incr k} {
       molinfo top set frame $k
       $all update
       set sel [atomselect top "protein and (name CA) and within 3 of (resname CUR and not hydrogen)"]
       set num1 [$sel num]
       set resid1 [$sel get resid]
       puts "number=$num1"
       puts "resid=$resid1"
}

Thanks
Nupur Bansal
Graduate Student
Merz Group
Michigan State University