There are two different errors occurring in HPF2. The first one will show up in stderr as:

[ERROR] Format error in frag file. Position: 51 Fragment: 49 Residue: 6
ERROR:: Exit at: .\fragments.cc line:723

This is due to a corrupt input file. The wu will error out in the beginning of the run. These wus are being patched now.

The second error will show up in stderr as:

<message>
Incorrect function. (0x1) - exit code 1 (0x1)
</message>
<stderr_txt>
ERROR:: Exit at: .\dock_structure.cc line:401

We are working on a fix.

Thanks,
armstrdj