Hello Dr. Steinbrt
I am playing around with couple of molecules calculating their absolute and
relative binding free energies.
I understand for absolute binding energy restraints play important role and
should be considered as first step in calculation as per your discussion on
mailing archive
http://archive.ambermd.org/201001/0202.html.
What will be your suggestion regarding relative energy stuff and What role
restraints play in it?? as your tutorial on benzene to phenol transformation
does not discuss anything about restraints.
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.
Kindly suggest if this much of fluctuation is fare enough while dealing
with large no. of atoms transformation?? or it is because of not applying
restraints?
Please find the plots as pdf this time.
Thanks a lot for your guidance
Best Regards
On Tue, Oct 5, 2010 at 4:01 PM, <steinbrt.rci.rutgers.edu> wrote:
> Hi,
>
> from what you send me it seems like you are removing a complete ligand to
> get the total binding free energy. That is a pretty advanced type of
> simulation and not easy to get to reasonably converged results. You
> probably have to introduce restraints at some point before your ligand
> diffuses away, plus getting a smooth vdW curve even for small ligands can
> be tricky. This is quite a complicated research project, so be sure to
> experiment a lot and follow other peoples work on the topic (B. Roux and
> M. Shirts groups come to mind among others)
>
> > I am also running few more lambda values for vdw decoupling in order to
> get better convergence.
>
> be prepared to make that many more and longer simulations...
>
> Sorry, but I couldn't see your attachment, as it's docx, but feel free to
> resend the curves in an open format,
>
> 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 Wed Oct 06 2010 - 00:30:02 PDT
