Hi Chris,
This is generally due to missing atoms in those residues.  If they had truncated side chains, there is an option in dock prep to fix that.  If they are missing backbone atoms, however, you'd have to add them some other way. However, these are not huge deviations of charge so if they aren't near some binding site or area that you really care that much about, the effect wouldn't be that large and you could choose to disregard.

Occasionally it will be due to unrecognized atom names, especially if you had hydrogens to start with, so you could also try removing all the original hydrogens and adding them back with dock prep.  However, the missing atoms situation is much more likely.

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Aug 17, 2023, at 10:33 AM, Chris Ellis via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
>
> Hi,
>
> After running the dock prep, I get the following warning in the reply log.
>
> Charges for residue MHS determined
> Total charge for #0: -79.622
> The following residues had non-integral charges:
>       VAL 124.A -0.2719
>       LYS 38.F 0.66
> 1 model(s) had non-integral total charge
> Details in reply log
>
> How can I fix this warning? Do I need to fix this?
>
> Thank you for any help you can provide. I truly appreciate it.
>
> Chris