Thales Kronenberger wrote > > Hello Everybody > > I'm running a production simulation of a kinase (after minimization > and equilibration) and after concluded 20ns I got the following > problem when I tryied to run g_rmsf > > "Fatal error: > Molecule in topology has atom numbers below and above natoms (4005). > You are probably trying to use a trajectory which does not match the > first 4005 atoms of the run input file. > You can make a matching run input file with tpbconv. > For more information and tips for troubleshooting, please check the > GROMACS > website at http://www.gromacs.org/Documentation/Errors" > > I insert ions in the PDB and ATP. My ion's topology were included as: > "#include "WT_Other_chain_A2.itp", #include "WT_Other_chain_B2.itp"". > I don't know if they're causing the trouble >
They aren't. But like the error message says, until you know what the coordinates in your trajectory file represent, and how that relates to the run input file you gave to g_rmsf it will be a mystery. Mark -- View this message in context: http://gromacs.5086.n6.nabble.com/Molecule-in-topology-has-atom-numbers-below-and-above-natoms-tp4999896p4999897.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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