[gmx-users] Glycoproteion MD

lloyd riggs lloyd.riggs at gmx.ch
Fri Aug 31 13:25:59 CEST 2012

Dear (sorry cant read chinese),

You can find some OPLS or 53a6 Parameters on the web by doing extensive searches, mostly they are free, but hosted on varied individual lab web sites.  That, or it may be easier to define some sets of bonds (angles, dihedrials, lengths charges, etc...from either the CRC or national institute of standards) for a small subset of sugars, inclusive of the inter-chain bonds, and then just use the defined names you gave the sugar atoms (ie Cc for sugar carbon, Pc for phosphorylated to sugar, etc... as inclusive this would only be several to a dozen atom types or somthing)....(then you can post it :-))...but it might be easier than trying to define things based on single sugar moieties available on the web, as you most likely would have errors when your suger moities are large from the inter-sugar bonds between subunits, such as a 10-20 length polysacharide on a glycosylated protein.  This is less trivial than it might seem, but would still take a few days, and you might be able to 
 use all but say 1-2 atoms if you find several defined parameters for sugars on the web already...


Stephan Watkins

-------- Original-Nachricht --------
> Datum: Fri, 31 Aug 2012 09:26:38 +0800
> Von: "陈应广" <525342307 at qq.com>
> An: "gmx-users" <gmx-users at gromacs.org>
> Betreff: [gmx-users] Glycoproteion  MD

> 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.
>  Thanking all

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