AMBER Archive (2004)

Subject: AMBER: about GLYCAM prep files in AMBER

From: Ozlem Demir (demir_at_qtp.ufl.edu)
Date: Tue Jul 20 2004 - 12:34:07 CDT

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

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu