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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Received on Mon Jul 06 2026 - 19:00:02 PDT
