On Sun, Oct 30, 2011, Urszula Uciechowska wrote:
>
> I need to run MD simulations for a protein with a modified
> glycopeptides inside. I was wondering if someone could give me some
> ideas how to prepare parameters/libraries for such as peptides.
Please see the link "Glycam parameters for carbohydrates" at the Amber web
site (
http://ambermd.org), which will take you to the Woods' lab site.
(We should update this link to indicate that it is the place to go for
glycoproteins as well as for carbohydrates.)
Section 3.5.3 of the AmberTools Users' Manual ("procedures for building a
glycoprotein in LEaP") should also help, as will section 2.8. (Again, the
titles for sections 2.8 and 3.5 mention only carbohydrates and lipids, but
actually deal with glycoproteins as well.)
....dac
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Received on Mon Oct 31 2011 - 06:00:03 PDT
