[AMBER] parameters for Lys-sugar

From: Urszula Uciechowska <urszula.uciechowska.chem.umu.se>
Date: Fri, 23 Mar 2012 13:15:38 +0100

Dear AMBER users,

I have a peptide with a sugar bound (beta-D-Glucose), and I would like to run MD on that with a protein later. I am trying to find a easy way to
generate the parameters for this part. I know that I could use a RESP-A1A charge model for the entire new residue and scaling factors for 1-4 interactions.
However I have no idea how to start with that ...
I was wondering if there is any tutorial for that?
Could anyone suggest me something? I attached a mol2 file of the residue with sugar bound.

Thank you in advance!

/Urszula

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Received on Fri Mar 23 2012 - 05:30:04 PDT
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