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<http://www.gromacs.org/mailman/listinfo/gmx-users>> 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 *>* *>* *>* _______________________________________________ *>* gmx-users mailing list gmx-users at gromacs.org<http://www.gromacs.org/mailman/listinfo/gmx-users> *>* http://www.gromacs.org/mailman/listinfo/gmx-users *>* Please search the archive at http://www.gromacs.org/search before posting! *>* Please don't post (un)subscribe requests to the list. Use the *>* www interface or send it to gmx-users-request at gromacs.org.<http://www.gromacs.org/mailman/listinfo/gmx-users> *>* Can't post? Read http://www.gromacs.org/mailing_lists/users.php *>* * -- 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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