[gmx-users] Whereabouts of NDLP???

ifat shub shubifat at gmail.com
Tue Feb 15 12:46:04 CET 2011

Was this server ever reestablished?
Is there a link which I can use to calculate the optimal box?
Ifat* *

Hi Alan,

Unfortunately there have been server problems (severe hacking) in
Groningen some while ago, and the NDLP server was terminated. But,
we're right about to reestablish an improved server here in Utrecht.
This server will be much faster, seconds rather than hours - the
optimal packing for the GroEL/GroES complex (60k atoms) took somewhere
around a minute maybe, and will also provide an optimal simulation
cell for a given ensemble (NMR, ENM, MD). In addition, the principal
author at the time was not in favour of adding the program to the
Gromacs suite, and there were some depency issues as well. I don't see
why the new program should not also become incorporated in Gromacs.

That being said, we still need a bit of time here to wrap things up.
In the mean time, as long as I'm not run over by requests, you can
send me a (few) structure(s) off the list, and I'll be happy to
calculate the packing.



On Sat, Mar 15, 2008 at 5:15 AM, Alan Chen <achen at
>* Hi All:
*>*  I recently came across  Tsjerk Wassenaar's JCC papers about  a
*>*  Near-Densest Lattice Packing
*>*  algorithm for choosing the optimal triclinic box for a non-spherical
*>*  macromolecule.
*>*  I have a rather cylindrical  RNA I am studying right now, and I wanted
*>*  to try out NDLP only the website referred to by the paper
*>*  no longer exists, and I can't find any reference to NDLP on the new
*>*  rug.nl homepage nor does google give me any clues. Does
*>*  anyone know as to this package's current whereabouts?
*>*  Thanks,
*>*  Alan Chen
*>*  _______________________________________________
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Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623
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