-in:file:fullatom is a Booloean flag – it’s either on or off, and doesn’t take a filename. To pass an input PDB file in, you’d use the -in:file:s option, so your commandline should be “… -in:file:fullatom -in:file:s 4hna_9_his.pdb …”
Thanks for your reply. Now the problem is with flags -max_helix_melt and -max_strand_melt. If I take the default values (-1), it is creating the loopfile with no LOOP information. How should I determine this to get the correct loopfile.