Hi Nahren –


I’m not a Tcl user, so I don’t know how you would accomplish this in Tcl.  However, you definitely you write a bash script that greps for the desired lines and then uses awk or sed to extract the values of interest.


Does anyone on the list know how to do this in Tcl?





From: nahren manuel [mailto:meetnahren@yahoo.com]
Sent: Thursday, June 10, 2010 5:17 AM
To: apbs-users@lists.sourceforge.net
Subject: Re: [Apbs-users] APBS on trajectory


Dear Nathan,
Generating input files is not a problem for me. But to read output from APBS is the problem.
 I have written a VMD-tcl script to generate the complex.pqr and complex.in for APBS runs. How do I save the values from APBS run into a variable. This is where I am stuck.

best regards,
- - -
#get the total number of frames
set nframes [molinfo top get numframes]
#complex, ligand & receptor, defined
set complex [atomselect top all]
set ligand [atomselect top "resid 1 to 432"]
set receptor [atomselect top "resid 433 to 849"]
puts "Total frames : $nframes"
set nframes 3
for {set nfr 0} {$nfr < $nframes} {incr nfr} {
# updating the coordinates to the current frames
$complex frame $nfr
$complex update
$ligand frame $nfr
$ligand update
$receptor frame $nfr
$receptor update
puts "FRAME: [expr $nfr + 1]"
$complex writepdb complex.pdb
$ligand writepdb ligand.pdb
$receptor writepdb receptor.pdb
#" pdb2pqy.py --apbs-input --ff=parse complex.pdb complex.pqr"
#set report [open {| df -k} RDWR]
#{pdb2pqr.py --apbs-input --ff=parse complex.pdb complex.pqr}
set r12 [open {| pdb2pqr.py --apbs-input --ff=parse complex.pdb complex.pqr} RDWR]
sleep 30
set r13 [open {| apbs complex.in > result.txt} RDWR]
sleep 150
#!pdb2pqr.py --apbs-input --ff=parse complex.pdb complex.pqr
#  for loop of $nfr ends
$complex delete
$ligand delete
$receptor delete


--- On Thu, 6/10/10, Baker, Nathan <Nathan.Baker@pnl.gov> wrote:

From: Baker, Nathan <Nathan.Baker@pnl.gov>
Subject: Re: [Apbs-users] APBS on trajectory
To: "nahren manuel" <meetnahren@yahoo.com>, "apbs-users@lists.sourceforge.net" <apbs-users@lists.sourceforge.net>
Date: Thursday, June 10, 2010, 5:51 AM

Hello –


This system is currently being moved while I change institutions.  I’m hopeful that someone else on the mailing list may have a copy of the scripts that you can use during the move.


Note that it is fairly straightforward to write scripts (bash, python, etc.) to generate APBS input files to calculate solvation energies for each of your snapshots.  Is that all you’re trying to do?






From: nahren manuel [mailto:meetnahren@yahoo.com]
Sent: Wednesday, June 09, 2010 6:31 AM
To: apbs-users@lists.sourceforge.net
Subject: [Apbs-users] APBS on trajectory


Dear APBS Users,

I would like to do MMPBSA calculation on my trajectory (generated with GROMACS).

How can i calculate the necessary energies for the coordinates in my trajectory.

Calculating the energy for 1 or 2 frames can be  done manually. But to automate the procedure (for the trajectory) I am sure there must be a simple way.

 I tried to write a TCL script in VMD but I am unable to store the result of APBS. Please instruct me.

I was making use of the tutorial few weeks back

but suddenly it does not open.

Warm regards,


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