Actually I figured it out. in forcefield.itp,
the nonbonded.itp file must be included before the bonded.itp file... On 2011-04-07 02:22:38AM -0500, Mark Abraham wrote: > On 7/04/2011 3:45 PM, Peter C. Lai wrote: > > 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? > > You need to be sure your grompp working directory also has the modified > forcefield file. The "include path" for filenames looks first in the > working directory and then in the directory indicated when you sourced > GMXRC. grompp's normal output (or maybe with -debug 1, or something) > probably says what it is doing. > > grompp -pp will write a post-processed stand-alone .top that you can use > to verify things got picked up correctly. However if grompp is failing, > that's probably not a help. > > Mark > > > 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... > > -- > 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 -- =============================================================== 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
