Hi Nahren --

Thanks for the reminder.  I'll work with the folks here to troubleshoot.

Thanks again,


On Wed, Feb 29, 2012 at 9:06 AM, Nahren Mascarenhas <mailnahren@gmail.com> wrote:
Hi Nathan,
Well the issue was that  atompotligand.txt and atompotprotein.txt, do not contain any atom potential values. Since I am doing a MM/PBSA type calculation (from a single simulation), I need to calculate the atom potentials , for (i) complex (ii) ligand and (iii) protein from a single trajectory.


On 02/29/2012 05:59 PM, Baker, Nathan wrote:

Hi Nahren –


The output looks reasonable; can you please remind me of the issue with this?




Nathan Baker
Pacific Northwest National Laboratory
Tel:  509-375-3997



From: nahren [mailto:mailnahren@gmail.com]
Sent: Sunday, February 19, 2012 11:06 AM
To: apbs-users@googlegroups.com
Subject: Re: [apbs-users] ATOMPOT protein-ligand complex


Dear APBS users,
The output (outputlog.log) is attached. It does say the following,
  Atom potentials to be written to atompotcomplex.txt
  Atom potentials to be written to atompotligand.txt
  Atom potentials to be written to atompotprotein.txt
The atompotcomplex.txt is also attached. The other two txt files,atompotprotein and  atompotligand just produced the following lines.

# Data from APBS 1.3