[gmx-users] forcefield

[Tsjerk Wassenaar]

Hi Lalitha,

Zebularine is beyond the trivial. You may be able to derive something
reasonable from the other bases using 'chemical intuition' (cytidine,
thymidine, uracil), but it's likely that the electronic structure of
the ring is too different to justify an approach like that. Likely you
should perform parameterization the proper way, which is not a
beginners subject. At least have a look at
http://www.gromacs.org/WIKI-import/Parametrization

Cheers,

Tsjerk

On Wed, Oct 14, 2009 at 7:30 AM, lalitha selvam <hayagrivar at hotmail.com> wrote:
> Hi,
>
> I want to do simulation with the ligand called zebularine. I dont find
> forcefied for that. Also i read prodgr has been deprecated..
> Could you please help me to find out the forcefield for the ligand
> zebularine.
> Thanks in advance
> lalitha
>
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-- 
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623