[gmx-users] Question about n-linked glycans

Laercio Pol Fachin laercio_pf at yahoo.com.br
Sun Sep 28 18:28:26 CEST 2014

Dear Mikhail,

If you are interested in a GROMOS-compatible force field for glycoproteins (and, consequently, N-linked glycans), we've just published new 
parameter sets for such biomolecules: http://onlinelibrary.wiley.com/doi/10.1002/jcc.23721/abstract

If you, or anyone else require any assistance, or have questions, please email me.

Best regards,
Laércio Pol Fachin

Em Domingo, 28 de Setembro de 2014 7:00, "gromacs.org_gmx-users-request at maillist.sys.kth.se" <gromacs.org_gmx-users-request at maillist.sys.kth.se> escreveu:

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Today's Topics:

   1. Re: position restrains while pull simulation (shivangi nangia)
   2. Question about n-linked glycans (Mikhail Yustanov)
   3. Re: Question about n-linked glycans (bipin singh)
   4. How to compute self diffusivities when the xtc trajectory
      file contains only a subset of atoms (rocwhite168)
   5. Re: How to compute self diffusivities when the xtc trajectory
      file contains only a subset of atoms (Mark Abraham)


Message: 2
Date: Sat, 27 Sep 2014 23:15:44 -0400
From: Mikhail Yustanov <mikhailyustanov at gmail.com>
To: "gromacs.org_gmx-users at maillist.sys.kth.se"
    <gromacs.org_gmx-users at maillist.sys.kth.se>
Subject: [gmx-users] Question about n-linked glycans
Message-ID: <53F7FED0-5F0D-4BBB-BC3E-B8C527B6DE3F at gmail.com>
Content-Type: text/plain;    charset=us-ascii

Hi all,

I am trying to study the influences of N linked glycans on protein stability. I am very new to MD Simulations. I wonder what is the best way to generate a topology file for the glycoprotein. Is there AMBER/GLYCAM integrated force field presently available? I have read through the basic and membrane tutorial but am still lost. 

Thank you,


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