AMBER forcefield and thioglycosides

From: Neil Whittemore <Neil.Whittemore_at_Colorado.EDU>
Date: Thu 05 Oct 2000 21:41:55 -0600

I have sent this to the computational chemistry list and not
received that many responses. Forgive the cross-posting,
but I would like to begin modeling these molecules as soon
as possible. Here is my question:

I am using the AMBER forcefield with the Homans carbohydrate

parameters (AMBER*) in the InsightII2000 package from MSI to

model glycosides. I would like to compare these models with

models of their thio-counterparts. What are people's
experience using AMBER * on thioglycosides? The major issue

with using these parameters is that there does not seem to
be a suitable parameter set/potential type for the sulfur
atom in the glycosidic linkage---the only ones relating to
sulfur I could find were for disulfides/methionine and

Any advice/comments would be greatly appreciated.

Neil Whittemore
Received on Thu Oct 05 2000 - 20:41:55 PDT
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