VMD-L Mailing List

From: Vermaas, Joshua (Joshua.Vermaas_at_nrel.gov)
Date: Mon Aug 22 2016 - 11:28:50 CDT

I mean, this should work as far as I can see. Is an error message being emitted, or is the selection empty so the files themselves are? Try something like this:

set filelist [glob *.PDB]
  foreach file $filelist {
    mol new $file
set name [file rootname $file]
set selp ["within 5 of type FE"]
puts [$selp num]; #This will print out the number of atoms in the selection.
$selp writepdb $name_FE.pdb
}

I'm guessing that for whatever reason the selection is empty, and you run into problems that way.

-Josh

On 08/21/2016 09:17 PM, Akshay Bhatnagar wrote:
Dear all

I want to find the residues within 5 angstroms distance around "FE" atom in 20 pdb files. Instead of loading the files one by one i am trying to acheive this through tcl script. But, the "within" command in not working on the tkconsole. My script is:

set filelist [glob *.PDB]
  foreach file $filelist {
    mol new $file
set name [file rootname $file]
set selp ["within 5 of type FE"]
$selp writepdb $name_FE.pdb
}

Can someone please help!!.

Thank you very much

With Regards
Akshay Bhatnagar
PhD Student
BITS Pilani Hyderabad Campus