In that case, AFFDO looks like the tool that you would want to use. I would
expect that at least one of the 5 corresponding authors would be
responsive, and several are also Amber developers so they may see your
message here. You might want to mention the specific problem that you are
having with that program.
On Sun, Oct 20, 2024, 3:27 PM Marawan Hussien <marawanhussain.yahoo.com>
wrote:
> I agree, while many factors play a role, torsional parameters consistently
> have a prominent effect. The impact of torsional parameters on
> ligand-protein binding free energies has been extensively discussed in
> numerous studies. For instance, the AFFDO paper:
> https://chemrxiv.org/engage/chemrxiv/article-details/66df56e9cec5d6c1429f22e9
>
>
> Additionally, several papers by John Chodera and others have highlighted
> similar observations.
>
>
>
> On Sunday, 20 October 2024 at 12:04:27 pm GMT-6, Carlos Simmerling via
> AMBER <amber.ambermd.org> wrote:
>
>
> 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
> >
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> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
> >
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Received on Sun Oct 20 2024 - 13:00:02 PDT
