On Wed, Jun 05, 2019, Melania T wrote:
>
>I have been using GAFF with the ff99SB forcefield for small organic
>molecules. Is this a reasonable setup to use?
>
>I know there is GAFF2, so that is an easy change... should I be using
>something other than ff99SB?
GAFF2 is recommended for small molecules. ff99SB is only for proteins,
and should definitely be updated to ff14SB (load leaprc.protein.ff14SB
in your tleap script.)
>
>The molecules are typically under 50 atoms, are mainly amines and ethanols.
If the above is true, than you would not be using either ff99SB or
ff14SB, since your molecules are not proteins.
>
>I am also interested in druglike molecules such as nitralin and caffeine
>etc, these are polar molecules with many rings inside them... Will the same
>methods be alright for them?
Depends on your definition of "alright": GAFF2 is the best (semi-)
automated solution that Amber offers. We have other programs (see
especially paramfit and mdgx) for the generation of bespoke force fields
for particular cases. And, alternatives to GAFF2 are increasingly being
developed in other codes. Molecules with partial conjugation are
frequently challenging to automated force field assignment protocols.
...good luck...dac
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Received on Thu Jun 06 2019 - 07:00:02 PDT
