VMD-L Mailing List

From: Davide Mercadante (dmer018_at_aucklanduni.ac.nz)
Date: Thu Aug 08 2013 - 16:08:12 CDT

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
>
>