On Fri, Jun 10, 2016, Miroslav Krepl wrote:
>
> 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.
Thanks for the report. We are looking into the origins of the behavior you
report, and will post something here as soon as we can. This email is just a
place-holder to indicate that we have not forgotten about your mail.
....regards...dac
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Received on Tue Jun 14 2016 - 05:30:03 PDT
