I am using gromacs 4.5.5, I didn't tell you yesterday. I have been tried a lot of things, but without any success.
One of that I think has to work fine, is with the NGLU nomenclature, but when I use it, I obtain this There is a dangling bond at at least one of the terminal ends and the force field does not provide terminal entries or files. Edit a .n.tdb and/or .c.tdb file. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors I am really sure about the structure of the Ligand ( Glu is in a separate chain like a ligand) so I don't know what to do. My PDB file looks like this ....... [...] ATOM 1896 OXT ALA A 258 -5.158 76.455 109.444 1.00 26.88 A TER HETATM 1932 N NGLU B 1 18.161 74.498 104.017 1.00 24.96 HETATM 1933 CA NGLU B 1 18.483 73.747 105.315 1.00 22.94 HETATM 1934 C NGLU B 1 19.769 73.978 105.618 1.00 27.29 HETATM 1945 O NGLU B 1 20.258 74.226 106.781 1.00 28.71 HETATM 1936 CB NGLU B 1 18.262 72.255 105.280 1.00 19.40 HETATM 1937 CG NGLU B 1 18.556 71.574 106.686 1.00 19.32 HETATM 1938 CD NGLU B 1 17.462 71.977 107.666 1.00 21.73 HETATM 1939 OE1 NGLU B 1 16.330 72.460 107.490 1.00 22.44 HETATM 1940 OE2 NGLU B 1 17.965 71.816 108.815 1.00 30.0 HETATM 1941 OXT NGLU B 1 20.862 74.195 104.777 1.00 27.10 END -- View this message in context: http://gromacs.5086.x6.nabble.com/Problem-with-Amber99SB-ILDN-ff-tp5009641p5009706.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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
