Hello, I know that is an already know problem but I don't know how to move on.
running pdb2gmx I had this message Fatal error: Atom CG is used in an interaction of type atom in the topology database, but an atom of that name was not found in residue number 163. Residue 163 is a GLY and has no a CG atom, here it is ATOM 1244 N GLY A 163 -81.506 20.445 -34.642 1.00 40.80 N ATOM 1245 CA GLY A 163 -80.353 20.498 -33.724 1.00 39.79 C ATOM 1246 C GLY A 163 -79.161 19.700 -34.239 1.00 38.24 C ATOM 1247 O GLY A 163 -78.044 19.744 -33.659 1.00 40.13 O This structure starts from 0 numbering residues, I had the same structure starting from -1, the error is the same, but now residue 163 is a GLN, here it is ATOM 1248 N GLN A 163 -79.370 19.001 -35.352 1.00 35.72 N ATOM 1249 CA GLN A 163 -78.318 18.161 -35.917 1.00 30.51 C ATOM 1250 C GLN A 163 -77.517 18.844 -37.005 1.00 30.20 C ATOM 1251 O GLN A 163 -78.027 19.724 -37.705 1.00 31.08 O ATOM 1252 CB GLN A 163 -78.886 16.891 -36.484 1.00 30.01 C ATOM 1253 CG GLN A 163 -79.580 16.003 -35.488 1.00 33.24 C ATOM 1254 CD GLN A 163 -79.783 14.619 -36.055 1.00 36.41 C ATOM 1255 NE2 GLN A 163 -79.630 13.601 -35.211 1.00 44.58 N ATOM 1256 OE1 GLN A 163 -80.100 14.464 -37.234 1.00 44.13 O I have tried both with OPLS-AA/L all-atom and CHARMM27 all-atom (with CMAP) - version 2.0 force fields, but the problem is still the same. Can anyone help me? Thanks -- gmx-users mailing list [email protected] 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 [email protected]. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
