I recently had some issues with re-ranking RosettaDock-generated decoys using ZRANK. The basic idea is described in a paper by Pierce and Weng, 2008 (http://www.ncbi.nlm.nih.gov/pubmed/18214977), where the authors used RosettaDock to refine docking predictions from ZDOCK, and then do a rescoring using ZRANK. Since ZRANK requires polar hydrogens to be added to all decoys before it performs rescoring, they stated in their paper "ZRANK was used to rerank the ZDOCK models as described previously, with polar hydrogens added to the unbound proteins using RosettaDock prior to scoring. For the refined structures, hydrogens were already in the structures from RosettaDock. The nonpolar hydrogens (which were also added by RosettaDock) were ignored by ZRANK.".
I thought it should be OK since I turned on -no_optH false flag during docking, so Rosetta should be able to optimize polar H positions. However the hydrogens seemed not to be recognized by ZRANK with this error "Warning: no hydrogens found in PDB file, need to include polar hydrogens for accurate scoring".
I noticed the authors used RosettaDock 2.0, different from the version I used (3.5). Not sure if this causes the problem. I also noticed that there are some differences in naming the H atoms than other programs that add polar H. I tried using Discovery Studio to add H, and it worked well with ZRANK. So I am wondering how to make the Rosetta hydrogens recognizable by ZRANK. Anyone have suggestions on this? Thanks in advance.