Others here have much more experience with ligand binding feee energies
(for example the York lab), but are you confident that torsion parameters
are the problem? Otherwise your subject line may lead people with expertise
in other areas to not read this. Many other aspects are important, such as
water model, protein model, ligand partial charges model, and of course
your free energy workflow.
On Sun, Oct 20, 2024, 1:13 PM Marawan Hussien via AMBER <amber.ambermd.org>
wrote:
> Dear Amber Users,
> I hope this message finds you well. I am reaching out to inquire if anyone
> is utilizing automated tools for torsional re-parameterization to refine
> GAFF/GAFF2 torsional parameters. From my experience, the tools available in
> AmberTools seem inadequate for large-scale applications.
> We have observed that using off-the-shelf GAFF parameters for
> ligand-binding free energy estimation can sometimes yield results that are
> even less accurate than docking.
> I would appreciate any insight or recommendations regarding successful
> workflows. I’ve come across the AFFDO code and reached out to the
> developers but have not received a response, so I’m turning to the
> community for alternative solutions.
> Currently, I rely on GROMACS tools, but the output I’m using isn’t easily
> portable to standard AMBER formats. Any suggestions or advice would be
> highly appreciated.
> Kind regards,Marawan
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sun Oct 20 2024 - 11:30:02 PDT
