Ok I'm now getting the dreaded "Unknown bond_atomtype CG2O5" grompp fatal error. I ran pdb2gmx on a pdb of my ligand and it generated a gro and a top file:
http://pastebin.com/HL3k7EPU for the gro http://pastebin.com/y6T4ir7y for the top I ran "grompp -f em.mdp -c nonanone.gro -p nonanone.top -o em.tpr" CG2O5 and all the other new atoms I added are in the appropriate atomtypes.atp file. The forcefield.itp file I added my custom #includes for the new parameters. How do I go about tracing this? the rtp is correct since it wouldn't have been able to map NNON to a gro and top file otherwise. Here is my forcefield.itp: http://pastebin.com/6dTKuqnG The two files I custom added were ffgenbonded.itp and ffgennonbonded.itp http://pastebin.com/xYvXtbzT http://pastebin.com/XXAbmvRH Any help would be greatly appreciated... -- =============================================================== Peter C. Lai | University of Alabama-Birmingham Programmer/Analyst | BEC 257 Genetics, Div. of Research | 1150 10th Avenue South p...@uab.edu | Birmingham AL 35294-4461 (205) 690-0808 | =============================================================== -- 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
