AMBER Archive (2007)

Subject: Re: AMBER: Re: how to create an O linked N-acetylglucosamine in a protein

From: Karl Kirschner (kkirschn_at_hamilton.edu)
Date: Tue Jul 17 2007 - 08:39:43 CDT

Hi Ming,

        The AMBER manuel outlines the use of the Glycam force field and prep
file (AMBER9 manuel pp. 22-29). Glycam work no differently that any
other force field or set of prep files. You would source the force
field and use the prep files just as you would when dealing with
amino acids or nucleic acids.

        The main points you need to keep in mind when preparing your
glycosylated protein is:
1) Make sure the carbohydrate residue names in the pdb file are name
appropriately (eg. 2MA, 3LB, -- p25 & 26) - this is how you use the
Glycam prep files.
2) If it is a branched glycan (eg. a-Man(1-->6)-[a-Man(1-->3)]-b-Man-
R), then you will need to include TER between the branches in the PDB.
3) If you have TER statements in your the glycan portion of your PDB,
then you will need to use the bond command in leap to create a
covalent bond between the residues.

If this doesn't make sense, I would suggest you first simplify your
system and troubleshoot your problems/questions there. Start by
reducing your glycosylated protein to just two linked carbohydrates
(note: you will need to add the methoxy group to the C1 position of
the first carbohydrate to replace residues you are removing). Once
you have this mastered, make a branched trisaccharide. Then try to
add the serine residue. Start with the basics and work up your
understanding to the large complicated system. The Glycam website
that Austin referred you to is a very helpful and useful site,
however it should not be used as a substitute for true understanding
of what you are doing when using AMBER. There are lots of tutorials
for how to prepare many different systems in leap; you can find these at

http://amber.scripps.edu/tutorials/ or http://www.conflex.co.jp/
prod_amber.html. Using the Glycam website is

Hope this helps.
Good luck,
Karl
____________________________________
Karl N. Kirschner, Ph.D.
Center for Molecular Design, Co-Director
Hamilton College, Clinton NY 13323
____________________________________

On Jul 16, 2007, at 11:44 PM, ming hui wrote:

> Dear all,
>
> I am trying to create and attach an N-acetylglucosamine to a
> serine residue in a protein, and I would appreciate any help on
> what is the procedure to do so? I'm afraid I just do not understand
> how to use Glycam in such a situation. And when are prep files
> required for carbohydrates?
>
> Thank you for your time
> Regards,
> Ming Hui
> (sorry for sending the incomplete message earlier by accident!)

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