Dear all,
I have a question regarding the ff14SB protein ff (the recommended
default) as implemented in AMBER. In some of my systems, it
seems to me that I am getting better results for tyrosine and phenylalanine
using the preliminary ff12SB
version.
It almost looks to me as if the new atom type describing the
phenylalanine and tyrosine CB atom (type 2C) was not implemented in the
residue files at all. There is discrepancy between the AMBER implementation
and the original literature describing the ff14SB.
As a result, I observe in simulations that the phenylalanine and
tyrosine behave in ff14SB similarly as with ff99SB. Their chi2 dihedral
profiles appear to be similar. The same issue is not present with the
ff12SB force field version which works differently and in my systems
better.
Does anyone have any experience with similar behavior?
Thank you and best wishes,
Miroslav Krepl
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Received on Fri Jun 10 2016 - 07:00:03 PDT
