I) What means "statistic value of parm94", where do these parameters come
from ... they are not mentioned in the "Development and Testing of a General
Amber Force Field" paper.
Since in AMBER protein force fields, many atom types are used for planar
carbons, while in gaff, only ca, cc, cd are used. Therefore we use mean
values for some force field parameters.
>
> II) Why are the values of the torsional potential for "single bonds" (X
> -cc-cc-X) and "double bonds" (X -cc-cd-X) in the aromatic system identical.
> Shouldnt there be a different torsional behavior ?
>
It is not a big deal at all for X-cc-cc-X and X-cc-cd-X sharing the same
torsional parameters since the four atoms always in a plane and a large
force constant of V2 term guarantee it is the case. While for the
conjugated chain systems, X-ce-ce-X and X-ce-cf-X take different parameters
since those four atoms may not necessary in a plane.
>
> Best
Junmei
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Received on Sun Mar 16 2008 - 06:07:49 PDT
