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.