Re: [AMBER] parameters for anchor-modified glycopeptides

From: FyD <fyd.q4md-forcefieldtools.org>
Date: Mon, 31 Oct 2011 17:59:29 +0100

Dear Urszula,

> 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.

You could follow approaches developed . q4md-forcefieldtools.org.
See for instance:
http://q4md-forcefieldtools.org/Tutorial/Tutorial-3.php
  &
http://q4md-forcefieldtools.org/Tutorial/Tutorial-3.php#28

You can find examples of glycoconjugates/glycopeptides in R.E.DD.B. as well:
http://q4md-forcefieldtools.org/REDDB/projects/F-85/
http://q4md-forcefieldtools.org/REDDB/projects/F-84/
http://q4md-forcefieldtools.org/REDDB/projects/F-72/
http://q4md-forcefieldtools.org/REDDB/projects/F-71/
All these projects are published & the references and PubMed
Identifier (PMID) are now available within each project.

If you provide a drawing or a structure of your glycopeptide we could
help more easily...

regards, Francois



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Received on Mon Oct 31 2011 - 10:00:02 PDT