Hi there, I am using GROMACS4.5.4 and the GROMOS 53A6 united-atom force field to do MD with my protein-ligand system.
I was trying to add aliphatic hydrogens to the .gro and .trr or .xtc trajectory file with g_protonate, but the Fatal error was: Library file in current dir nor not found ffgmx2in defalt directories. Then re-name the directory in ../share/top/gmx2.ff to ffgmx2, and this time g_protonate seems to be able to find those .hdb files. But another error follows as: Reading frames from gro file 'Protein in water', 66743 atoms. Reading frame 0 time 0.000 Opening force field file ffgmx2/aminoacids.hdb Opening force field file ffgmx2/atomtypes.atp Atomtype 1 Opening force field file ffgmx2/aminoacids.n.tdb Opening force field file ffgmx2/aminoacids.c.tdb Segmentation fault I searched for 'Segmentation fault', nothing relevant to g_protonate came up. So I wonder if anyone could kindly help me out? Or is there an easy alternative way to protonate the trajectory file? Thanks a lot for your attention. Yun -- 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