First check your .gro file and your .top file, to make sure atom 6518 (or Water) is consistently defined.
Next step would be to make sure this atom features in the index file within a "correct group". In some cases, if a single atom is left out and not part of any group in the index file, it gives this error. Why not make your index file again ? Read the help provided with the command "make_ndx" to understand this. Hope that works! -----Original Message----- From: [email protected] on behalf of Kieu Thu Nguyen Sent: Fri 1/4/2013 6:51 AM To: Discussion list for GROMACS users Subject: [gmx-users] error with indexfile Dear All, When using the command grompp -f equi.mdp -c membedded.gro -p merged.top -n index.ndx -o equilibrate.tpr The error is Fatal error: Invalid atom number 6518 in indexfile How can i fix this ? Thank so much for any help ! Regards, KT -- gmx-users mailing list [email protected] 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 [email protected]. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing list [email protected] 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 [email protected]. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
