[gmx-users] grompp -r again

[David]

On Thu, 2002-10-03 at 17:40, hugo verli wrote:
> Thanks, David.
> 
> But I am using for now a system of just one sugar ring to test the conversion.
> However, I need to apply this transformation to a polyssacharide system
> complexed to one protein, so the system syze will became prohibitive to free
> enegy perturbation, dont'it?
Not necessarily. If you only want to modify a single ring in the whole
sugar chain it should still work, at least if the binding mode remains
the same.
> Besides the two conformations coexist in solution, so the energy barrier between
> them should not be soo high. 
Well, that both exist means that the free energy difference is not very
large; the barrier may be in principle, although it doesn't seem too
likely in this case.


-- 
Groeten, David.
________________________________________________________________________
Dr. David van der Spoel, 	Biomedical center, Dept. of Biochemistry
Husargatan 3, Box 576,  	75123 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://zorn.bmc.uu.se/~spoel
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