Good day!

Sorry for the late reply.

Yes, I read this article but what confuses me is that during the minimisation steps I'm offered two possible ff for a ligand -- AM1-BCC and Gasteiger.

So, basically what you are saying is that both atom charges and atom types are assigned using GAFF, not AM1-BCC?

Could you explain that in a little more detail? For example, here (http://ambermd.org/antechamber/ac.html#atomtype) it says that an atom type in antachamber might be assigned either by GAFF or by AM1-BCC or by other ff. And do I understand correctly that within antachamber there are only two possible ways to assign charge and those are AM1-BCC and Gasteige?

Correct me if I misunderstood you.

Best regards,

Sergey Vladimirov.

On Sat, May 23, 2020 at 12:47 AM Elaine Meng <meng@cgl.ucsf.edu> wrote:

Hi Sergei,
It already is. That is, if your system includes a nonstandard residue like some ligand, then Chimera automatically uses Ambertools/Antechamber to generate GAFF parameters to use in minimization and/or dynamics.

This is all described in the Minimize Structure manual page, see the section on "Force Field Parameters":
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/minimize/minimize.html>

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

> On May 22, 2020, at 12:29 PM, Сергей Владимиров <sergei.vladimirov@chemistry.msu.ru> wrote:
>
> Good day!
>
> My name is Sergei Vladimirov, I'm a student at Moscow State University.
> As far as I know, when running a molecular dynamics of ligand-protein interaction one must use different force fields to the ligand and the protein. There is a mm14ff to calculate interactions within a protein but there are only two different force fields to calculate interactions within a ligand.
> I've been led into believing that the best ff for small organic ligands is GAFF.
> So my question is, is there any way to implement the GAFF force field into the production of molecular dynamics?
>
> Is there anything I'm missing? I will be awaiting your reply.
>
> Best regards,
> Sergei Vladimirov.