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PIPER-FlexPepDock protocol file missing

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PIPER-FlexPepDock protocol file missing


I've been trying to run the PIPER-FlexPepDock pipeline in both ways, following the steps in the documentation page (, and using the scripts in the "tools/peptide docking" folder. But both cases need the script "" which doesn't exist in the source. Where can I get this script or any equivalent?

Thank you in advance.

Post Situation: 
Thu, 2021-11-04 06:33

Hello Mariela,

Some further details would be appreciated-

Are you trying to run the full rosetta protocol using one of the binaries like 


Such as FlexPepDocking.mpi.linuxgccrelease, or a mac binary, etc.?

Using any of these binaries should not rely on any external scripts, python or otherwise.


The scripts under tools/peptide_docking are for running another protocol called PIPER-FlexPepDock, and assumes you have the PIPER software (by schrodinger) installed and licensed.

You can see the full instructions for running the protocol in the README file located in the 'peptide_docking' folder you mentioned.

Please note that the address to download PIPER has changed and it can be found here:


I hope this helps!

Fri, 2021-11-05 01:56

Hi zivben,

Thanks for your response!

I've been trying to run the PIPER-FlexPepDock protocol. I already installed PIPER from the older version (ClusPro) and from Schrödinger after your suggestion. Until now, I managed to run the Rosetta protocol as in until  Step II: Running PIPER FFT docking, so PIPER is working. But in the next step (Step III: Top scoring 250 PIPER models are extracted) it needed the script ""  that is absent in both versions of PIPER installed.

Could you help me with this script?

Best regards.

Fri, 2021-11-26 05:11