[Chimera-users] Molecular dynamics

[Elaine Meng]

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 at 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.