Hi,
for relative binding energies you should not need restraints, as there are
always real parts of the molecules anchoring it in place.
> The maximum dv/dl rmsf in above example of yours is 3.655, where as the
> two
> ligand which I am dealing with shows maximum rmsf of approx 11 with the
> transformation of 14 unique atoms.
Thats not a small change, so the larger rmsf looks reasonable to me. It
depends on what you want to get out of your data to judge if that is
acceptable.
> Please find the plots as pdf this time.
your vdW curves look a bit bumpy still, be prepared to run more lambda
points, especially at higher l-values. are you using the softcore module
for the vdW changes?
Kind Regards,
Thomas
Dr. Thomas Steinbrecher
BioMaps Institute
Rutgers University
610 Taylor Rd.
Piscataway, NJ 08854
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Received on Wed Oct 06 2010 - 06:00:03 PDT
