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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Received on Thu Apr 28 2011 - 06:30:07 PDT
