The AMBER manual also contains lots of good information on the topic.
GLYCAM is made to treat most oligosaccharides well in most
biologically-relevant contexts. We are constantly tweaking the behavior of
the force field and adding functionality. If you develop a new force field
for a specific molecule in a specific situation, you will get better
results for that molecule in that situation. The results will not
necessarily apply anywhere else. It is also necessary to be careful how
you validate any new force field.
On Sat, Oct 29, 2016 at 6:27 AM, FyD <fyd.q4md-forcefieldtools.org> wrote:
> Dear Nikolay,
>
> > I'm going to conduct MD simulation for protein molecule
> > which has some covalently bound oligosaccharide residues.
> > Should I treat these residues separately by the specially designed
> > forcefield (e.g. GLYCAM) ?
>
> You might be interested in a work about glicoconjugates reported in
> REDDB...
> http://q4md-forcefieldtools.org/REDDB/projects/F-85/
> In my opinion the approach to follow to design your FF is highly
> related to the oligosaccharide structure itself...
>
> regards, Francois
>
>
> F.-Y. Dupradeau
> ---
> http://q4md-forcefieldtools.org/FyD/
>
>
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>
--
:-) Lachele
Lachele Foley
CCRC/UGA
Athens, GA USA
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Received on Sat Oct 29 2016 - 13:30:02 PDT
