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 edited 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 And gromacs get me: opening force field file /usr/local/gromacs/share/gromacs/top/oplsaa.ff/atomname2type.n2t There are 23 names 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 for more information and tips for troubleshooting, ………………………………………………….. I copied all of files in oplsaa.ff folder in my working directory and edited the atomname2type.n2t file as the above mentioned in my working directory. How to solve my problem? Why do gromacs open / usr/local/gromacs/share/gromacs/top/oplsaa.ff/atomname2type.n2t? 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
