Hello –


I would recommend using the same grid dimensions for all PQR files to ensure consistent results.


Good luck!


Nathan Baker
Pacific Northwest National Laboratory
Tel:  +1-509-375-3997



From: Shahar Sukenik [mailto:shaharsu@gmail.com]
Sent: Monday, April 23, 2012 3:16 AM
To: apbs-users@googlegroups.com
Subject: [apbs-users] Electrostatic energy of protein folding




I want to calculate the change in free energy upon peptide folding using APBS to account for the electrostatics. I have a large ensemble of folded and unfolded PQR's to do this with.

Do I have to use the same grid dimensions for all the PQR's? Or can I take ensemble averages for the charging free energy and use those instead to calculate the difference?

Does anyone know of a paper that deals with these kinds of calculations?