Hi Ifat, It has: http://haddock.chem.uu.nl/Squeeze/
Cheers, Tsjerk On Tue, Feb 15, 2011 at 12:46 PM, ifat shub <shubi...@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 >> >> >> _______________________________________________ >> gmx-users mailing list gmx-users at gromacs.org >> 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. >> 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 > > > > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- 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 -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
