Dear Dr Steinbrecher,
Thanks alot for your kind reply !
Well, from this discussion i came in conclusion the i shall calculate
relative binding energy of methyl fucose wrt fucose as descrived in tutorial
for phenol wrt benzene. This wil be a small transformation of methyl group
in the fucose ring. Could you suggest me the timespan for minimization,
equil and production phase. Should I try with given input files in tutorial
or this was just for teaching purpose, and i shuold try longer run in first
ateempt ?
Thanking u
sushil
On Fri, Jan 15, 2010 at 9:59 AM, <steinbrt.rci.rutgers.edu> wrote:
>
>
> well, just give it a try, you can always ask me (or better even, the Amber
> list) if something seems to go wrong. I would strongly suggest you start
> with a simple problem, e.g. changing one sugar into another by a small
> chemical change, to get a really good feel about what TI can and cant do.
> Once you are really confident about getting relative energies right, you
> can move on to computing absolute ones.
>
> > Do u have any other ideas af evaluation binding energy using mm/qm
> > approaches ? I will be highly obligued to fing your help in doing this
>
> I dont think much has been done in that direction, in my personal opinion,
> MM- forcefields are better at computing interaction energies than any QM
> method you can afford to do on a protein-ligand complex.
>
> Kind Regards,
>
> Dr. Thomas Steinbrecher
> BioMaps Institute
> Rutgers University
> 610 Taylor Rd.
> Piscataway, NJ 08854
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Jan 15 2010 - 01:30:02 PST
