AMBER: about GLYCAM prep files in AMBER

From: Ozlem Demir <>
Date: Tue, 20 Jul 2004 13:34:07 -0400 (EDT)

Hi All,

I started using AMBER recently and I need to model an enzyme and its
substrate. The substrate is alpha(2,3) sialyl lactose. I have tried GLYCAM
prep files and creating a new UNIT with the sequence OME 4GA 3LB 1SA but
in fact what I need is OH 4GA 3LB 1SA sequence. How can I form this one? I
could not find a prep file for OH group.

My other question is about atom types. In the pdb file of the enzyme do I
have to change the atom types so they match with the ones in the GLYCAM
prep files?

The last question : After a new unit is created using the above sequence,
where can I find the optimum glycosidic torsion angle values to correct
the conformations?

Thanks in advance,

Ozlem Demir

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Received on Tue Jul 20 2004 - 18:53:00 PDT
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