Hi Nahren --
Thanks for the reminder. I'll work with the folks here to troubleshoot.
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?
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
# ATOM POTENTIALS