Hi,
> ATOM 1 1HO ROH 1 2.144 0.950 -0.364 1.00 0.00
> ATOM 2 O1 ROH 1 1.184 0.950 -0.364 1.00 0.00
> ATOM 3 C1 0fA 2 1.154 -0.437 -0.084 1.00 0.00
> ATOM 4 H1 0fA 2 2.168 -0.866 -0.126 1.00 0.00
> ATOM 5 O5 0fA 2 0.313 -1.155 -0.937 1.00 0.00
Do you have to treat the hydroxyl group as a separate residue? Maybe that
is a glycam convention, but why not call the whole sugar 0fA? This
shouldn't affect your results, though.
> (ROH.O1) to methyl-fucose ":OME.O". So should i also include this atome
> during the transformation and I shold go for transformation --OH to --OCH3
The transformation -OH to -OCH3 should in the limit of sufficient sampling
give the same free energy change as -H to -CH3 with O as common atom in
both states. Depending on the different convergence and sampling of both
cases, you will get slightly different results, though. I personally would
not include the O in both scmasks, but either approach would be valid.
Doing both is also a nice way to check for convergence of your results.
Kind Regards,
Dr. Thomas Steinbrecher
BioMaps Institute
Rutgers University
610 Taylor Rd.
Piscataway, NJ 08854
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Received on Fri Jan 15 2010 - 09:30:06 PST
