Dear GMX users, To generate a topology file for an arbitrary molecule (TP) on graphite surface, I used g_x2top program to generate “TP.itp” file and I manually construct "graphite.itp" file.
Generated topology file is as the following: #include "./oplsaa.ff/forcefield.itp" #include "TP.itp" #include "graphite.itp" [ system ] TP ON GRAPHITE [ molecules ] ;molecule name nr. TP 2 grap 6400 ……. And the graphite.itp is as the following: [ moleculetype ] ; name nrexcl grap 1 [ atoms ] ; nr type resnr residu atom cgnr charge 1 opls_145 1 grap C 1 0.000 I run grompp for EM with this command line: grompp -f *.mdp –c *.gro -p *.top -o *.tpr It gave me the following error: ……… Fatal error: Syntax error - File ffnonbonded.itp, line 1 Last line read: '[ atomtypes ]' Invalid order for directive atomtypes For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors ……. I know things in the [ molecules ] section need to line up with what's in the *.gro file. Also I looked at that link but I don’t know how to solve this problem. And other question is: Do I need to make “nonbonding.itp” to insert in topology file for introducing nonbonding interaction of graphite with TP molecule? Sincerely 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
