[gmx-users] glycosylated residues

Maik Goette mgoette at mpi-bpc.mpg.de
Tue Jan 17 12:29:49 CET 2006


First: It would be helpful to know, which FF you'll use.
Second: If you use PRODRG, it "just" produces GMX-FF-parameters at the 

So, if you want to use GMX-FF, then just create your molecule with PRODRG.

If you use AMBER- or OPLSAA-FF, you can do, what I always do in those 
situations...Intuitive (NO, not intelligent!) design...;)

Take the ribose from RNA as a template and start "guessing" values, 
which seem probable.
The correct way to do it, would be gaining parameters from QM, though.

Sorry, that this isn't much help, but better this, than nothing. ;)


Maik Goette, Dipl. Biol.
Max Planck Institute for Biophysical Chemistry
Theoretical & computational biophysics department
Am Fassberg 11
37077 Goettingen
Tel.  : ++49 551 201 2310
Fax   : ++49 551 201 2302
Email : mgoette[at]mpi-bpc.mpg.de
WWW   : http://www.mpibpc.gwdg.de/groups/grubmueller/

Lars Meinhold wrote:
> Hi
> I would like to perform MD on a protein which has
> some residues glycosylated (sugar added to amino acid):
> N-glycosylated ASN (Asparagine)
> O-glycosylated SER (Serine)     
>                THR (Threonine)
> However, I could not find any force-field parameters
> for the sugars in the gromacs package. I found parameters
> for a sugar (NAG - acetylglucosamine) using PRODRG.
> Can I easily bind the amino-acid and this sugar?
> Which parameters should I use for the bonds?
> e.g., for the ASN-NAG I'm stuck with the following bond:
>                     H       to sp3 carbon
>                     |     /
>  to a 'HCOH'group - N - C - to a '-O-C' oxygen
>                         |
>                         H
> Can anyone suggest a solution?
> Thanks a lot, Lars.
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