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Subject:
Re: Gromacs parameters
From:
Jodi Hadden <[log in to unmask]>
Reply To:
Users of GLYCAM & GLYCAM-Web <[log in to unmask]>
Date:
Fri, 30 Oct 2015 15:51:29 -0400
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As far as I know, the only way to use GLYCAM parameters in GROMACS is to build your files normally with AmberTools tleap, then convert the files to GROMACS format with the glycam2gmx.pl script from this reference:

Wehle M, Vilotijevic I, Lipowsky R, Seeberger PH, Varon Silva D, Santer M. Mechanical Compressibility of the Glycosylphosphatidylinositol(GPI) Anchor Backbone by Independent Glycosidic Linkages. J Am Chem Soc. 2012;134(46):18964–18972.

I successfully ran a GLYCAM simulation for a carbohydrate-only system in GROMACS a few years ago using this strategy, though I can't speak for building a system that contains both protein and carbohydrate.

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