Date: Tue, 16 Aug 2011 11:34:59 -0700
Hi all,
I have a small molecule that consists of a Thr with an ACE cap, a modified
(CO becomes CH2) Phe, and a rhamnose linked to Phe via a thio-glycosidic
linkage. And please see attached the molecule I drew.
While the Thr and Rha are the standard building blocks of GLYCAM06 and 99SB
force fields respectively, what about the modified Phe and the
thio-glycosidic linkage?
As what seemed to be discussed before in the archive, GAFF can be applied to
the entire molecule. But the sugar ring is very sensitive to dihedral
parameters, right? So the GAFF parameters (and am1-bcc charges) may not be
good enough for sugar?
Thus, I wonder if it's possible to add all the bond, angle, dihedral, and
charge parameters for the modified Phe and the thio-glycosidic linkage by a
.frcmod file. But where can I find proper parameters for thio-glycosidic
linkage? Could anyone tell me the steps (formats) to construct such a
.frcmod file?
Any help is appreciated!
Thanks,
Yun Shi
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