Ligand docking error Could not find essential file trigger-00001.ligand_docking_protocol

[Anonymous]

Hello,

My attempts at ligand docking on Rosie (e.g. job 26146)  keep failing after less than 15min. I am getting no input error. The json logs return the error:

"log": "nCould not find essential file trigger-00001.ligand_docking_protocol/score.sf in DB!n", 

I used Frog2 to generate my ligand sdf file and Chimera to estimate the starting x,y,z coordinates.

Any hints at what I might be doing wrong?

 

thanks,

Isabelle

[Anonymous]

You’re using “ADP” as the chain for the ligand. Chains should be a single letter (this is the PDB chain ID that the ligand will be placed into the ligand as.) – in practice, just leave this as X, unless your protein already has a chain X. (Even then, it’s better to change your protein such that the protein chain is something other than X.)

Error reporting on Rosie can leave things to be desired at times, but often one can  click the “[Full set of decoy structures created on this run (FS view)]” link, and then “logs” in order to see the run logs. In this case, although nothing is printed in the “error” logs, in the “output” logs, at the very bottom is the relevant error message. (“Error: getOption: key= ligand_chain stream extraction failed! Tried to parse ‘ADP'”) Not too illuminating, but at least it points you in the direction of the chain designation.

[Anonymous]

Many thanks for the reply, this is very helpful. I have resubmitted my job (ID=26200).

So it crashed again with the error

Could not find essential file trigger-00001.ligand_docking_protocol/score.sf in DB!

My ligand chain is ‘X’. The .ligand_docking_protocol_trigger.output.99.log shows:

protocols.rosetta_scripts.RosettaScriptsParser: Defined mover named "start_from" of type StartFrom

Error: ERROR: Exception caught by rosetta_scripts application:'Translate' mover: chain 'X' does not exist.

Error:

Isabelle

[Anonymous]

Eeek! It looks like a recent Rosetta update broke some of the functionality ROSIE ligand docking was using.

I’m trying to fix it now, and will see if we can get ROSIE updated as soon as we can.

[Anonymous]

The ROSIE ligand docking application has been updated, and it should work for you now, if you re-submit.

[Author]

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