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
> _______________________________________________
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> 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 - 09:30:03 PDT
