[gmx-users] Charges and Antechamber

[João Henriques]

Hi!

If your goal is to generate the atomic partial charges for a new
residue/molecule (not existing in the FF you are interested in using), then
doing the QM calculations is a must in most cases. For example, AMBER FFs
have a well documented and specific recipe you can easily follow, which
involves deriving the electrostatic potential from QM calculations at a
specific level of theory + basis sets and then using the RESP fit procedure.

Cornell, Wendy D., et al. "A second generation force field for the
simulation of proteins, nucleic acids, and organic molecules." Journal of
the American Chemical Society 117.19 (1995): 5179-5197.

I've done this a couple of times and it was relatively simple. I never
needed to use antechamber for anything else, all modelling and assignment
of atom types were done manually. Exotic species might make things more
complicated.

P.S.: For non-AMBER FFs you need to follow their own recipes/methods. For
example, GROMOS FFs don't have a fixed recipe for obtaining the charges
(you can even set them by hand according to your own whim), but the
calculations must reproduce solvation enthalpies, etc. In sum, check the
original literature on the FF you plan on using to understand how to
calculate your own charges in a way that respects that specific FF's
"philosophy".

Hope it helps,
João



On Tue, Oct 3, 2017 at 3:16 PM, Sergio Manzetti <
sergio.manzetti at fjordforsk.no> wrote:

> Hi, I was wondering what the best approach is to simulate a negatively
> charged topology imported from ANTECHAMBER (which can't do integral
> charges):
>
> 1. Do QM calculations on the molecule, then edit the output from
> Antechamber
>
> or
>
> 2. Do something else.
>
> Sergio Manzetti
>
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