Atom potentials

[srihas29]

Hello APBS developers,

I would like to point out two bugs that I came across. I was testing it on a simple molecule ALA-ASP-ASP-ALA to write out the atom potentials using focusing.

1. During focusing it writes out really high potentials around e+18 for atoms which are close to the grid but slightly outside, ideally it should write zero.
2. I have observed quite a jump in the potential values going from initial calculation to a couple of focusing steps which results in really high electrostatic energies.

Platform:
Ubuntu 22.04 LTS
APBS Version 3.4.0 - compiled from source
apbs_files_srihas.zip

I am attaching the files here, with a bit of explanation :

A:3:ASP-ASP.xst-ASPP_APBS.in - This is the apbs input file (please ignore the naming convention )
A:3:ASP-ASP.xst-ASPP_APBS.pqr - The pqr file used for the calculation
AO_A:3:ASP-ASP.xst-ASPP_(1-6).txt - These are the atom potential files generated using focusing

If we look at the 6th potential file, it contains a potential value of -7.401206e+18, this atom is exactly at the boundary of the grid (probably outside).

Also, if we compare the 1st and 6th file there are atoms where the the difference in potential is by a factor of 10^4 which might be a problem.

Please get back if you need more information.

Regards,
Srihas Velpuri, Master's student
Chair of Theoretical and Computational Biochemistry (Prof. Dr. Matthias Ullmann),
University of Bayreuth, Germany