Hi all,
I need to parametrize a ligand that is a tripeptide blocked with
terminal groups that are not available in the Amber parameter
database:
Boc-Gly-Arg-Arg-AMC (see:
http://www.chemexper.com/chemicals/supplier/cas/113866-14-1.html)
Where:
Boc = t-butiloxy-carbonyl
AMC = 7-amine-4-methyl-coumarin
Could someone suggest what would be the best way to do it? I
considered just using antechamber for it, but since the amino acids
are available in the regular force fields, I imagine it could be best
to just use those parameters for the amino acids. Is that correct? If
this is the case, what would be the best procedure to parametrize the
terminal groups? What should I do to ensure a good description of the
bonds/angles involving both terminal group and amino acid atoms?
I'd appreciate any suggestions/links/references here.
Thanks a lot,
Gustavo.
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu May 19 2011 - 13:30:03 PDT
