I'm trying to dock 2 proteins in Rosetta dock serve (http://rosettadock.graylab.jhu.edu/) but it always has this problem:
This job failed to produce results. The RosettaDock Server support team has been notified.
Most failures result from departures from the PDB standards in the input file or from missing or spurious atoms. Please inspect your input file for irregularities and contact us if you need further support.
But I don't know how to solve this problem. I've check my 2 proteins, they are maybe OK, but I'm not sure.
Please give me some recommendations.
When I loaded your PDBs in a text editor, they came up in DOS mode - they've got Microsoft Windows line-break encoding rather than Linux/Unix encoding. I'm guessing that since the server is running Linux, it needs the Linux encoding.
I've attached a sanitized (and combined) PDB for you, give it a shot.
Great. My job has been finished. Thanks in advanced.