AMBER Archive (2005)

Subject: AMBER: Glycam-parameters and antechamber

From: Michele Porro (michele.porro_at_unibas.ch)
Date: Wed Sep 14 2005 - 11:06:42 CDT

Hello dear amber community,
                                               just a brief question.
I would like to perform an MD simulation of a disaccharide (GlcNAc-Gal)
that carries some modifications (basically protecting groups like Bz)
at two positions of the Gal moiety. Obviously I would like to still
make use of the GLYCAM parameters...
I know that in principle I should calculate RESP charges for this new
moiety and so on...but I don't have so much time & PC-power...
I was therefore thinking to use antechamber, calculate AM1-BCC charges,
editing the atomtype manually (and change them to the
glycam-conventions) and then, after having setup the system, perform
my MD simulation to obtain some clue about the conformation of this
modified disaccharide.
Would that be at least a rough estimation of the result I would by
doing it "correctly"??
Thanks for you help

mike

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