Hi
Thanks a lot for your guidance.Ya I am using soft core potential for Vdw
Decoupling and already running more lambda values for better convergence
On Wed, Oct 6, 2010 at 6:18 PM, <steinbrt.rci.rutgers.edu> wrote:
> 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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SUNITA GUPTA
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Received on Thu Oct 07 2010 - 05:30:03 PDT
