Re: [AMBER] parameters for anchor-modified glycopeptides

From: Urszula Uciechowska <urszula.uchiechowska.chem.umu.se>
Date: Tue, 1 Nov 2011 09:49:48 +0100

Dear Francois,

Thank you for your reply, I attached two of my peptides in pdb format file,
could you please have a look on them. I am reading the tutorial 3 but i guess that my peptides are more complex.
Could you suggest me something, how to start with them? Where to put the intra-molecular charge constrains in this case?

Thank you in advance

regards, Urszula
  
________________________________________
Von: FyD [fyd.q4md-forcefieldtools.org]
Gesendet: Montag, 31. Oktober 2011 17:59
An: AMBER Mailing List
Betreff: Re: [AMBER] parameters for anchor-modified glycopeptides

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 Tue Nov 01 2011 - 02:00:03 PDT