[gmx-users] How to protonate a gmx trajectory?

[Yun Shi]

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