VMD-L Mailing List

From: Nupur Bansal (nupur.b298_at_gmail.com)
Date: Mon Oct 07 2013 - 15:42:15 CDT

Hi,

No, I did not get any error then.

Thanks
Nupur

On Oct 7, 2013, at 4:38 PM, John Stone <johns_at_ks.uiuc.edu> wrote:

> Hi,
> I noticed that you have netcdf within angle brackets, which may be
> the source of your problem. Do you get any error when you run just the
> "mol new" and "mol addfile" commands in your script by hand?
>
> Cheers,
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Mon, Oct 07, 2013 at 04:28:04PM -0400, Nupur Bansal wrote:
>> 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
>
> --
> NIH Center for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> http://www.ks.uiuc.edu/~johns/ Phone: 217-244-3349
> http://www.ks.uiuc.edu/Research/vmd/