VMD-L Mailing List

From: Daniel Fellner (dfel694_at_aucklanduni.ac.nz)
Date: Wed Mar 30 2022 - 02:13:08 CDT

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