Hello Dr. Steinbrecher,
>From our earlier discussion I is clear that larger fluctuation is fare
enough when transforming quite large groups of atoms, but again I am not too
sure about the final results......ie. whats the reliability of the result if
its value is coming out to be in the range of +-10?
Thanks
On Thu, Oct 7, 2010 at 5:46 PM, sunita gupta <sunita.bio.gmail.com> wrote:
> 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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SUNITA GUPTA
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Received on Mon Nov 08 2010 - 22:30:02 PST
