On Wed, Mar 13, 2019, Träg, Johannes wrote:
>
>i have a problem with the gaff2 atom types cc and cd. According to the
>gaff2.dat file (Version 2.1, April 2016) cc and cd are identical.
>Consequently, the bond section of the gaff2.dat file includes the same
>parameters for cc-cc and cd-cd (340.18,1.426). However, the bond section
>also includes the bond cc-cd, but with different parameters
>(416.13,1.373). Due to the identity of cc and cd, this makes no sense to
>me. Which parameters are the 'right' ones?
What you report is correct and expected. From the original gaff paper
J Comput Chem 25: 1157–1174, 2004:
"both cc—cc and cd—cd are conjugated single bonds, and cc—cd is
conjugated double bond."
There is more explanation in the paper cited above that may help in
understanding the issues here. Basically, having both "cc" and "cd"
atom types is needed to make up for the fact that Amber (and gaff) don't
have the concept of a "bond order".
...hope this helps....dac
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Received on Wed Mar 13 2019 - 17:00:02 PDT
