[Chimera-users] Molecular dynamics

[Сергей Владимиров]

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.
>
> 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.
>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20200531/b9e5a7a5/attachment.html>