Solved

When i run the set vdw for the score function: scorefxn.set_weight(vdw, 1.0) and then attempt to score a pose scorefxn(pose) i get a fatal error in the VDW_Energy. When VDW is set to 0 it goes away. The scorefxn was working fine until I added a proline to my AA sequence.
I receive the following after running scorefxn(pose)
Etable 53 46 1 8
error: Fatal Error in VDW_Energy
error: Exit from: core/scoring/methods/VDW_Energy.cc line: 169

Hi all,

I am running ligandDocking application thru rosetta_scripts app. On the documentation "Rosetta Ligand Docking with Flexible XML Protocols", there is a paragraph addressing how to analyse the result.
The example can be downloaded from "http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0020161" in the supplement info.
I did exactly what it says on the example folder provided in the documentation but there is error relating to the residue type:

ERROR: Attempting to add a residue type with name 'CP1' but this name is already taken.

Dear fellows,

thank you for the newly rewritten version of make_fragments.pl in Rosetta 3.4 ... it came just in time when I was struggling with the old one! In my hands/case though, there was a problem with the inclusion of secondary structure prediction from pre-calculated files. (It worked well when files were calculated on the fly with psipred / SAM installed.)

I'll try to be exact with my description of the errors in the current version:

Dear fellows,

thank you for the newly rewritten version of make_fragments.pl in Rosetta 3.4 ... it came just in time when I was struggling with the old one! In my hands/case though, there was a problem with the inclusion of secondary structure prediction from pre-calculated files. (It worked well when files were calculated on the fly with psipred / SAM installed.)

I'll try to be exact with my description of the errors in the current version: