I don`t know about -h but -cl BLAHBLAH.pdb works for sure… you should also provide cutoff (most standard is around 0.3) by -cutoff 0.3 Mehmet -- View this message in context: http://gromacs.5086.x6.nabble.com/g-cluster-tp5014116p5014393.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com.