I am attempting to dock a peptide onto a protein using flexpepdock. The docking completes and the identified structures are plausible solutions. However, when I examine the score.sc file, I notice that the I_hb term has a single, extremely high value for all structures:
I_hb = 18446744073709551616.000
I am prepacking the structure before docking:
FLEXPEP -s PEPTIDE.pdb -flexpep_prepack -ex1 -ex2aro -overwrite
FLEXPEP -s PEPTIDE_0001.pdb -pep_refine -ex1 -ex2aro -nstruct 100 -lowres_preoptimize -native PEPTIDE_0001.pdb
Are the hydrogen bonds being properly calculated? Is there anything I should do to the structures to make sure h-bonds are taken into account?