VMD-L Mailing List

From: Gumbart, JC (gumbart_at_physics.gatech.edu)
Date: Thu Mar 31 2022 - 10:51:07 CDT

With regards to your first question, yes, absolutely it helps. But if an atom is completely buried, it’s definitely less sensitive to the water interactions, but not completely immune. The danger though is that it ends up as a “dumping ground” for excess charge while the more accessible atoms get optimized. Note that RESP suffers from the same problem. We discussed such challenges in this paper: https://urldefense.com/v3/__https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5980237/__;!!DZ3fjg!qLKMT80wQzM-4j2gR3n8Xew_oq3Z7ilwEoyQrK-Su31agpUhsdpBVIE-LZZPCwq4vw$

We ultimately settled on a combination of RESP and Natural Population Analysis, with the latter for the buried charges.

Best,
JC

On Mar 30, 2022, at 3:13 AM, Daniel Fellner <dfel694_at_aucklanduni.ac.nz<mailto:dfel694_at_aucklanduni.ac.nz>> wrote:

Just had a few questions about charge optimisation for a difficult substrate.

If the atom in question is entirely solvent-inaccessible but has hydrogens attached, does the inclusion of target data from those hydrogens aid in fitting the occluded atom? I've seen this done in the EtOH tutorial but have read conflicting information.

As for occluded atoms with no hydrogens attached, how can these be optimised? The highest penalties in my compound are on entirely occluded (SASA <0.020 nm^2/mol) atoms. Is there any sense including them in the charges to be optimised without any target data?

Daniel Fellner BSc(Hons)
PhD Candidate
School of Chemical Sciences
University of Auckland
Ph +64211605326