[gmx-users] Whereabouts of NDLP???

Tsjerk Wassenaar tsjerkw at gmail.com
Tue Feb 15 13:04:37 CET 2011

Hi Ifat,

It has: http://haddock.chem.uu.nl/Squeeze/



On Tue, Feb 15, 2011 at 12:46 PM, ifat shub <shubifat at gmail.com> wrote:
> Hi,
> Was this server ever reestablished?
> Is there a link which I can use to calculate the optimal box?
> Thanks,
> 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.
> Best,
> Tsjerk
> On Sat, Mar 15, 2008 at 5:15 AM, Alan Chen <achen at artsci.wustl.edu>
> wrote:
>> 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.
>> http://www.informatik.uni-trier.de/~ley/db/indices/a-tree/w/Wassenaar:Tsjerk_A=.html
>>  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
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Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands

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