<div dir="ltr"><div>Hi,</div>
<div>Was this server ever reestablished?</div>
<div>Is there a link which I can use to calculate the optimal box?</div>
<div>Thanks,</div>
<div>Ifat<em> </em></div>
<div> </div>
<div> </div>
<div> </div>
<div> </div>
<div>Hi Alan,<br><br>Unfortunately there have been server problems (severe hacking) in<br>Groningen some while ago, and the NDLP server was terminated. But,<br>we're right about to reestablish an improved server here in Utrecht.<br>
This server will be much faster, seconds rather than hours - the<br>optimal packing for the GroEL/GroES complex (60k atoms) took somewhere<br>around a minute maybe, and will also provide an optimal simulation<br>cell for a given ensemble (NMR, ENM, MD). In addition, the principal<br>
author at the time was not in favour of adding the program to the<br>Gromacs suite, and there were some depency issues as well. I don't see<br>why the new program should not also become incorporated in Gromacs.<br><br>
That being said, we still need a bit of time here to wrap things up.<br>In the mean time, as long as I'm not run over by requests, you can<br>send me a (few) structure(s) off the list, and I'll be happy to<br>calculate the packing.<br>
<br>Best,<br><br>Tsjerk</div>
<div> </div>
<div>On Sat, Mar 15, 2008 at 5:15 AM, Alan Chen <<a href="http://www.gromacs.org/mailman/listinfo/gmx-users">achen at artsci.wustl.edu</a>> wrote:<br>><i> Hi All:<br></i>><i><br></i>><i> I recently came across Tsjerk Wassenaar's JCC papers about a<br>
</i>><i> Near-Densest Lattice Packing<br></i>><i> algorithm for choosing the optimal triclinic box for a non-spherical<br></i>><i> macromolecule.<br></i>><i> <a href="http://www.informatik.uni-trier.de/~ley/db/indices/a-tree/w/Wassenaar:Tsjerk_A=.html">http://www.informatik.uni-trier.de/~ley/db/indices/a-tree/w/Wassenaar:Tsjerk_A=.html</a><br>
</i>><i><br></i>><i> I have a rather cylindrical RNA I am studying right now, and I wanted<br></i>><i> to try out NDLP only the website referred to by the paper<br></i>><i> no longer exists, and I can't find any reference to NDLP on the new<br>
</i>><i> <a href="http://rug.nl">rug.nl</a> homepage nor does google give me any clues. Does<br></i>><i> anyone know as to this package's current whereabouts?<br></i>><i><br></i>><i> Thanks,<br></i>><i> Alan Chen<br>
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Biomolecular NMR, Bijvoet Center<br>Utrecht University<br>Padualaan 8<br>3584 CH Utrecht<br>The Netherlands<br>P: +31-30-2539931<br>F: +31-30-2537623<br><br><br></div></div>