Dear Justin I want a topology for an arbitrary molecule (44 atom) and I use x2top program that .n2t file is it’s input.
The .pdb file is as the following: ATOM 1 O5 TPT 1 -6.131 -0.245 0.000 0.000000 ATOM 2 C21 TPT 1 -5.041 0.384 0.000 0.000000 ATOM 3 O6 TPT 1 -5.040 1.814 0.000 0.000000 ATOM 4 H12 TPT 1 -5.945 2.134 0.000 0.000000 ATOM 5 C18 TPT 1 -3.708 -0.387 0.000 0.000000 ATOM 6 C19 TPT 1 -2.374 0.383 0.000 0.000000 ATOM 7 H10 TPT 1 -2.373 1.453 0.000 0.000000 …… I copied oplsaa.ff folder in my working directory atomname2type.n2t file is as the following: O opls_267 -0.495284 15.9994 1 C 0.1214 C opls_470 0.594326 12.0110 3 C 0.1487 O 0.1306 O 0.1214 O opls_268 -0.560735 15.9994 2 C 0.1306 H 0.0974 H opls_270 0.417334 1.0079 1 O 0.0974 C opls_145 0.037549 12.0110 3 C 0.1487 C 0.1387 C 0.1387 C opls_145 -0.145422 12.0110 3 C 0.1387 H 0.1087 C 0.1395 H opls_146 0.110842 1.0079 1 C 0.1087 …… I used these command: ] g_x2top –f .pdb –o .top -pbc –ff oplsaa But I get: opening force field file /usr/local/gromacs/share/gromacs/top/oplsaa.ff/atomname2type.n2t There are 23 name to type translations in file oplsaa.ff Generating bonds from distances... atom 44 Can not find forcefield for atom C21-2 with 3 bonds Can not find forcefield for atom C18-5 with 3 bonds Can not find forcefield for atom C16-10 with 3 bonds Can not find forcefield for atom C20-11 with 3 bonds Can not find forcefield for atom C15-17 with 3 bonds Can not find forcefield for atom C12-18 with 3 bonds Can not find forcefield for atom C7-27 with 3 bonds Can not find forcefield for atom C5-28 with 3 bonds Can not find forcefield for atom C3-33 with 3 bonds Can not find forcefield for atom C2-34 with 3 bonds Can not find forcefield for atom C9-40 with 3 bonds Can not find forcefield for atom C10-41 with 3 bonds Program g_x2top, VERSION 4.5.4 Source code file: g_x2top.c, line: 206 *Fatal error:* Could only find a forcefield type for 32 out of 44 atoms. How to solve my problem. Why do gromacs open / usr/local/gromacs/share/gromacs/top/oplsaa.ff/atomname2type.n2t? I copyied oplsaa.ff folder in my working directory. Also I edited .n2t file in my folder. Thanks in advance, Afsaneh -- 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
