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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Received on Tue Nov 15 2016 - 08:30:02 PST
