Ok. I'm sure I get along somehow without the perl version since I just have
to modify the input for the minimization step.
Cheers,
Olli
Am 28.04.2011 17:59 schrieb "Jason Swails" <jason.swails.gmail.com>:
>
> I think I'd tend to agree with Markus on this one (although Ryde's MM/PBSA
> papers use the perl version). I'm not sure how you would go about
> accomplishing the buffer region in the nab program, and I'm pretty sure
Ryde
> et. al. used the nmode program as well.
>
> All the best,
> Jason
>
> On Thu, Apr 28, 2011 at 6:18 AM, Oliver Kuhn <oak.amber.googlemail.com
>wrote:
>
> > Again, Jason,
> >
> > I can remember I have asked something similar few month (or maybe a year
;)
> > ago.
> > I would like to use the method from:
> > An improved method to predict the entropy term within the MMPBSA
approach,
> > Kongsted Ryde, J Comput Aided Mol Des 2009
> >
> > The main reason is that it will be more computationally efficient and
I'm
> > interested how the distribution of entropy estimates will be compared to
> > usual NMA.
> >
> > The method minimizes a truncated 8A environment around the ligand but
with
> > a
> > 4A fixed buffer region.
> > Thus, I would tend to input a traj with the 12A environmental residues
> > around the ligand to the NMA routine in the MMPBSA.py script.
> > Can you suggest an easy way to tell the script to keep the 4A buffer
region
> > fixed during minimization - in other words, where do I have to change
the
> > code and set restraints?
> >
> > And b.t.w. thanks also to Bill and Carlo for the discussion on the usage
of
> > internal dielectric 1,2,4.
> >
> > Regards,
> > Oliver
> >
> > --
> > Oliver Kuhn, Department of Bioinformatics,
> > Center for Medical Biotechnology, University of Duisburg-Essen,
> > Universitätsstr. 1-5, 45141 Essen, Germany
> > phone +49 201 183-3121, oliver.kuhn.uni-due.de
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
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Received on Thu Apr 28 2011 - 09:30:10 PDT
