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Hello Clemens-- Please note that this mailing list is for Xplor-NIH, not CNS. But please see below for suggestions. > I am a rookie and working on my first NMR structure determination and > have to deal with a protein-ligand complex. The protein side is nicely > defined with cyana and I have transferred everything over to CNS in > order to dock the completely buried ligand (as segid B). I used xplo2d > to create both toplogy and parameter files of the ligand (a nucleotide > with sugar-ring and base). If I read in a pdb.file of the ligand with > protons, it throws them out to create .top and .par file. I really > would prefer to have them back in but don't know how. Do I have to use > the Hbuild function (I don't know in which interface and where to > find/how to run it)? hbuild still requires topology information. Perhaps the prodrg server is better than xplo2d at generating proton information? http://davapc1.bioch.dundee.ac.uk/programs/prodrg/ You will need the protons to get an accurate structure. best regards-- Charles -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.6 (GNU/Linux) Comment: Processed by Mailcrypt 3.5.8+ <http://mailcrypt.sourceforge.net/> iD8DBQFGc/L8PK2zrJwS/lYRAsxiAJ41wJKHskC6uIYQ5OphA2dTC3U1kQCggxHY p9iVgYmMLGrKRHGws8pOLDg= =Z41k -----END PGP SIGNATURE-----
