Hi,
You can have a look at openff bespokefit:
https://github.com/openforcefield/openff-bespokefit
Although it is not GAFF, openff forcefields are compatible with amber
and you can directly export parameters gromacs or amber topology. I used
bespokefit reparametrized ligand parameters in both amber and gromacs
for RBFE calculations.
best regards,
Juraj
On 21. 10. 24 12:08, Nikolay N. Kuzmich via AMBER wrote:
> Hi, sorry for the invasion,
> but I also wrote to request AFFDO software about 4 weeks ago and they did
> not reply either...
> Kind regards
> Nick
>
> Carlos Simmerling via AMBER <amber.ambermd.org> schrieb am So., 20. Okt.
> 2024, 10:52 PM:
>
>> 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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Received on Mon Oct 21 2024 - 04:00:02 PDT
