On 2011-04-07 02:01:47AM -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" > > On what line of what file? Please copy and paste the whole error > message. Keeping information back only hurts you :-)
Here is the entire message. It doesn't give me a line number in the mdp file NOTE 1 [file em.mdp]: For energy conservation with switch/shift potentials, rlist should be 0.1 to 0.3 nm larger than rcoulomb. ------------------------------------------------------- Program grompp, VERSION 4.5.4 Source code file: toppush.c, line: 631 Fatal error: Unknown bond_atomtype CG2O5 For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors ------------------------------------------------------- > > Mark > > > 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... > > -- > 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
