VMD-L Mailing List

From: Daniel Fellner (dfel694_at_aucklanduni.ac.nz)
Date: Fri Apr 01 2022 - 02:52:01 CDT

Oh great, thanks! I didn't realise RESP was suitable for deriving
CHARMM-compatible partial charges. I did notice FFTK has a RESP option now
but I thought it was just for AMBER.

I assume the procedure is to put static restraints on the aliphatic and
aromatic hydrogens not adjacent to a heteroatom (as per CHARMM protocol)
and to any atoms you don't need to optimise? I gave it a try just now, and
it does a good job for most atoms, though I do notice some unphysical
charges on the buried atoms. I guess I'll set these with NPA first.

Regarding the QM level of theory, should I stick to the default HF/6-31G*
for both the RESP and NPA calculations? My molecule is neutral and contains
only C, H, N, F, O atoms unlike the metal complexes in your paper.

Thanks again for your help,

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

On Fri, 1 Apr 2022 at 04:51, Gumbart, JC <gumbart_at_physics.gatech.edu> wrote:

> 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!oYXnkowufs7O21LPLJDcEZu-sUyKW1djm2q768uxznnYsiFZc6Hz08KflfEhk9Vtwg$
>
> 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>
> 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
>
>
>