Dear Urszula,
If I understood your molecule this is a beta-D-Glucose bound to the
Epsilon carbon of a Lysine residue with a new asymmetric carbon at
C_Epsilon. Interesting...
You could create a dipeptide for this pseudo lysine and follow the
approach described .
http://q4md-forcefieldtools.org/Tutorial/Tutorial-3.php#25
You could use the RESP-C2 charge model, but this means a mixture of
AMBER/GLYCAM scaling factors for 1-4 non-bonded interactions...
Considering that you have a Gluco configuration you could also use the
RESP-A1A charge model for this entire new residue - this also means
applying Amber scaling factors for 1-4 interactions.
The approach is described .
http://www.ncbi.nlm.nih.gov/pubmed/21792425 & is far more simple than
the first one...
regards, Francois
Quoting Urszula Uciechowska <urszula.uciechowska.chem.umu.se>:
> Dear Amber users,
>
> I would like to get the parameters for sugar which is bound to a
> peptide molecule. I am new to this and I was wondering if there are
> already available
> parameters that I could directly use or should I prepare them
> somehow by myself ? using antechamber or other program?
> I attached the pdb file,
> Thank you in advance for any suggestions.
>
>
> best regards
>
> /Urszula
>
> Umea University
> Department of Chemistry
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Jan 25 2012 - 07:30:03 PST
