Dear Dr. Simmerling,
Sorry for the late reply and thank you for sharing your insight.
Best regards,
Hoa Thanh Le
On Wed, Jul 8, 2026 at 8:52 PM Carlos Simmerling <
carlos.simmerling.stonybrook.edu> wrote:
> The water model can have an important contribution to binding affinities,
> since the water-ligand and water-receptor interactions are replaced with
> receptor-ligand interactions upon binding. I would look into the ligand
> binding affinity literature and see if benchmarking has been done for these
> water models. It goes beyond what works well in protein MD.
>
>
> On Mon, Jul 6, 2026 at 9:55 PM Hòa Lê <vnlethanhhoa.gmail.com> wrote:
>
>> This is the first time you received an email from this sender (
>> vnlethanhhoa.gmail.com). Exercise caution when clicking links, opening
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>> Dear Mr. Simmerling,
>>
>> Thank you for your reply.
>> May I ask a follow-up question: TIP3P-FB and OPC3 could replicate water
>> properties better than TIP3P. Would it be fine to use them with ff14SB and
>> ff19SB?
>>
>> Best regards,
>> Hoa Thanh Le
>>
>>
>> On Mon, Jul 6, 2026 at 9:13 PM Carlos Simmerling <
>> carlos.simmerling.stonybrook.edu> wrote:
>>
>>> I do not recommend using ff99SB, it is not quite old and has been
>>> replaced.
>>> the choice between ff14SB and ff19SB is somewhat related to which water
>>> model you will use - ff14SB is better suited for the old and less
>>> accurate TIP3P model. ff19SB should *never *be used with TIP3P, and
>>> works best with OPC water.
>>> Since TIP3P has been around much longer than OPC, there are more studies
>>> testing it for small molecule binding affinities, but there are quite a few
>>> with OPC as well. Since that's not a focus in my lab, I recommend looking
>>> at that literature.
>>> But you can tell your teammate that ff99SB should not be used in any
>>> case.
>>>
>>>
>>> On Sat, Jul 4, 2026 at 11:17 PM Hòa Lê via AMBER <amber.ambermd.org>
>>> wrote:
>>>
>>>> EXTERNAL EMAIL - This email was sent by a person from outside your
>>>> organization. Exercise caution when clicking links, opening attachments or
>>>> taking further action, before validating its authenticity.
>>>> Dear AMBER community,
>>>>
>>>> My team would like to use the Amber force field and GAFF to simulate
>>>> several complexes of protein-drug molecules. For the protein, my
>>>> teammate
>>>> wants to use Amber ff99SB, claiming that this force field has been
>>>> historically validated for protein-drug systems. But I would like to
>>>> take
>>>> the advantage of ff14SB in terms of more accurate backbone and side
>>>> chain
>>>> parameters. And I believe that ff19SB is even better. Has there any
>>>> benchmark for ff99SB, ff14SB and ff19SB for protein-drug systems? If
>>>> not,
>>>> theoretically, which force field among these choices should be more
>>>> accurate for such systems?
>>>>
>>>> Best regards,
>>>> Hoa Thanh Le
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>>>> https://protect.checkpoint.com/v2/r01/___http://lists.ambermd.org/mailman/listinfo/amber___.YzJ1OnN0b255YnJvb2s6YzpnOjUwYTgwOTNiMTE2M2UwM2QzYTc2MjIwNDcwNmQxYTQyOjc6YjRhYzpiYWQyNzhlMmZlYjE4YzczN2NkYTQ4OWU4MWIzMGE4ZWExYzZkYzJmODA5MmUyN2RjMDE3ZTM3N2E4NjRlYWRkOnA6VDpG
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Received on Sun Jul 12 2026 - 05:00:02 PDT
