[gmx-users] Glycoproteion MD

Laercio Pol Fachin laercio_pf at yahoo.com.br
Fri Aug 31 15:00:44 CEST 2012


If you can't find parameters for glycoprotein's MD for charmm27, OPLS or Amber99 (and GROMOS is an alternative for you), we've been working on MD simulations with this class of biomolecules, using GROMOS96 43A1 force field, as described:

Pol-Fachin, L.; Fernandes, C.L.; Verli, H.: GROMOS96 43a1 performance on the characterization of glycoprotein conformational ensembles through molecular dynamics simulations. Carbohydrate Research 344 (2009) 491–500.
Fernandes, C.L.; Sachett, L.G.; Pol-Fachin, L.; Verli, H.: GROMOS96 43a1 performance in predicting oligosaccharide conformational ensembles within glycoproteins. Carbohydrate Research 345 (2010) 663–671.

Best regards,
Laércio Pol-Fachin

Message: 1
Date: Thu, 30 Aug 2012 21:32:00 -0400
From: Justin Lemkul <jalemkul at vt.edu>
Subject: Re: [gmx-users] Glycoproteion  MD
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Message-ID: <50401410.7070500 at vt.edu>
Content-Type: text/plain; charset=UTF-8; format=flowed

On 8/30/12 9:26 PM, 陈应广 wrote:
> Dear all  I am interested in simulating a model of Glycoproteion. I could'nt
> find the define of the residue in any forcefield .rtp file of GMX. I am using
> Gromacs 4.5.5 . If any one can help me in getting forcefield parameters for
> charmm27/ OPLS/Amber99 in gromacs format please respond. Please suggest where
> else I should search for these.

If they haven't already been derived (and thus likely published), then you'll 
have to derive them yourself in a manner consistent with the original force field.




Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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