VMD-L Mailing List

From: Thomas C. Bishop (bishop_at_latech.edu)
Date: Fri Aug 09 2013 - 09:30:32 CDT

I often use the following loop for frame by frame analysis
Is there a better way?

load trajectory
set numframes [molinfo top get numframes]
set selected [atomselect top "some selection" ]
 for {set i 0} {$i < $numframes} {incr i } {
  puts "writing/analyzing frame $i"
  $selected frame $i
  $selected writepdb tmp.pdb
  DO YOUR ANALYSIS ON TMP.pdb
  CLEAN UP
}
 quit



On 08/08/2013 04:08 PM, Davide Mercadante wrote:
Hello Giota,

I guess that a simple bash script that iterates over a set of coordinate files extracted from your trajectory would work fine...
If you have command line apbs and pdb2pqr you can do the following:

from your trajectories dump a series of pdb files (that I will call $i) and then iterate like the following:

for i in *;
do
pdb2pqr [options] $i $i.pqr
apbs apbs.in
done

Your apbs.in file can be created by pdb2pqr or you can have a template that you can modify at each iteration using sed...

for example:

cat apbs.in | sed -e 's/what you want to substitute here/what you want that gets substituted here/g' > apbs_$frame$i in the script above apbs.in changes to apbs_$frame$i.

Knowing the name of your files should be very easy..

Hope this helps.

Cheers,
Davide

On 8/08/13 9:56 PM, PANAGIOTA KYRIAKOU wrote:

Hello,

I have a trajectory file of 5000 frames and I want to calculate the charge distribution for each frame, using the APBS program inside vmd. 
But I do not want to do it manually. 
I want to write a tcl or python script that will produce a pqr file and run ABPS for each frame.
Is it possible to use the APBS plugin through a script, and if so how?

Thank you in advance,
Giota

  

Panagiota Kyriakou

Graduate Student

Dept. of Chemical Engineering and Materials Science

University of Minnesota