PIPER-FlexPepDock protocol file apply_ftresult.py missing

[Anonymous]

Hello,

I’ve been trying to run the PIPER-FlexPepDock pipeline in both ways, following the steps in the documentation page (https://www.rosettacommons.org/docs/latest/application_documentation/docking/flex-pep-dock), and using the scripts in the “tools/peptide docking” folder. But both cases need the script “apply_ftresults.py” which doesn’t exist in the source. Where can I get this script or any equivalent?

Thank you in advance.

[Anonymous]

Hello Mariela,

Some further details would be appreciated-

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

FlexPepDocking.{ext}.{distribution/compiler}release

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:

https://www.schrodinger.com/products/piper

 

I hope this helps!

[Anonymous]

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 https://www.rosettacommons.org/docs/latest/application_documentation/docking/flex-pep-dock 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 “apply_ftresult.py”  that is absent in both versions of PIPER installed.

Could you help me with this script?

Best regards.

[Author]

Posts