it's difficult to give a completely general answer to this question since
it does depend on details. This is a bit of a long answer just so it's in
the archive. The short answer if you don't want to read on is that using an
older cofactor with ff14SB should not be a problem, we have done this
before.
To get more details... In most cases this should be fine, the charge model
and vdw parameters have not changed. it's always good to check things over,
though, and make sure there are no issues in the leap log file. you might
also want to look over the atom types and make sure there are no conflicts
between new ones that may have been created for the 3rd party parameter set
and those in the ff14SB set.
that's the general answer. However, there are definitely cases where this
will not work as expected, such as with modified amino acids that probably
have the atom types from ff99SB. In ff14SB, amino acid backbone atom types
were changed, so the phi/psi parameters that would get applied to the
standard amino acids would be different from those applied to the modified
one (even if the modification is not related to the backbone). As a simple
example, if you simulate a protein with standard amino acids and then
compare to the same protein with a modified amino acid, part of the
difference will be due to the modification, and part may be due to the
change of parameter set for the non-modified part. Fixing this can be
difficult, since you might get combinations of atom types that were not
present in either force field separately.
If all of that isn't clear, then my answer would be that if it isn't a
modified amino acid (like the cofactor that you mention), you should be
fine. If it is a modified amino acid, then you'll need to be very careful
about how to integrate the 2 models. Doing nothing will probably work in
the sense that it will generate data, but it might be difficult to
interpret. Getting it properly fixed would not be that difficult, but it
would require some knowledge of how the force fields work.
carlos
On Tue, Nov 15, 2016 at 11:12 AM, DmitryASuplatov <genesup.gmail.com> wrote:
> Dear Amber users,
>
> Amber parameters for non-standard amino acids, ligands, cofactors etc.
> are available from third-parties. In most cases, these parameters "are
> suitable for use with the FF94 and/or FF99 force fields", as specified
> by the authors.
> E.g., the FF99 parameters for NADH/NAD are available in the Richard
> Bryce Database.
>
> However, the currently recommended default forcefield in Amber is
> FF14SB, which is an update of the FF99SB according to the publication.
> Maier JA, Martinez C, Kasavajhala K, Wickstrom L, Hauser KE, Simmerling
> C. ff14SB: improving the accuracy of protein side chain and backbone
> parameters from ff99SB. Journal of chemical theory and computation. 2015
> Jul 23;11(8):3696-713
>
> My Question:
> Can I use FF14SB to model my protein together with third-party
> parameters marked suitable for FF99/FF99SB, e.g. for a cofactor?
>
> Thank you.
> Best,
> Dmitry
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>
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Received on Tue Nov 15 2016 - 08:30:03 PST
