[Chimera-users] Molecular dynamics

[Elaine Meng]

Hi Sergey,
The partial atomic charges are calculated by the AM1-BCC method or Gasteiger method, as specified by you.

The other parameters are GAFF.  GAFF does not include include charges.

> 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>

" Minimize Structure uses the GAFF types to associate nonstandard residues with parameters other than charges."

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 31, 2020, at 12:54 PM, Сергей Владимиров <sergei.vladimirov at chemistry.msu.ru> wrote:
> 
> 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 at 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.
> 
> 
> 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.
> 
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