[gmx-users] ligand topology

[az kalsom]

hi

i have docked the compund with protein and selected the best protein-ligand
conformation for simulations,
but when i generate the topolgy for ligand by

Automated Topology Builder (ATB) and Repository , job is killed every tym.
error message is 1) geometry was inappropriate; (2) the number of hydrogen
atoms or the net charge was inappropriate...

what should i do to remove this ?

regards