Hi Nick,
I had looked at the tool in the past, and the installation and running process wasn't a smooth experience. However, I’ll give it another try and see if there have been any improvements.
That being said, I still have concerns about compatibility, particularly regarding non-bonded parameters. Ideally, GAFF should be compatible with the AMBER family and its associated water models. There’s no guarantee that an external force field will behave in the same way, and the risk here is that these types of incompatibilities are often silent. You’ll get results, but whether they're accurate within the approximation limits of any force field is hard to say.
Interestingly, they seem to recognize this issue, which is why they created a standalone force field for both proteins and small molecules. I believe it was called " Rosemary" though I haven’t been able to find an official repository or documentation. Still, it might be worth trying out.
Thanks,Marawan
On Monday, 21 October 2024 at 04:42:50 am GMT-6, Juraj Dobias via AMBER <amber.ambermd.org> wrote:
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 - 09:30:03 PDT
