Rosetta Ligand Ensemble

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    • May 26, 2021 at 5:21 pm #3774
      Anonymous

        Dear Rosetta community, 

        In our group we are interested in using the RosettaLigandEnsemble (RLE) protocol  (https://doi.org/10.1021/acsomega.7b02059). 

        Since we are new to Rosetta, we decided to start by executing the RLE protocol with the example input files provided with the Rosetta source code

        (i.e. /PATH/TO/ROSETTA/main/demos/protocol_capture/rosettaligand_ensemble/)

        We are using Rosetta (release 2021.07, March 4th 2021; in particular 2021.07+release.c48be26)

        using the following command:

        /PATH/TO/ROSETTA/main/source/bin/rosetta_scripts.linuxgccrelease -database /PATH/TO/ROSETTA/main/database/ @inputs/options -docking:ligand:ligand_ensemble 0 -nstruct 2

        Afterwards, we received this error message:

        Error: Element ‘TransformEnsemble’, attribute ‘optimize_until_ideal’: The attribute ‘optimize_until_ideal’ is not allowed.

        Unfortunately, we were not able to find the documentation regarding the ‘TransformEnsemble’ mover and the associated ’optimize_until_ideal’ parameter.

        Therefore, we decided to run a test removing ‘TransformEnsemble’ it to see if Rosetta is able to proceed without this option. 

        Here, Rosetta was able to successfully parse the input files but we encountered another problem: Segmentation fault (core dumped). 

        If necessary I can forward you the “ROSETTA_CRASH.log”.

        One additional thing we noticed: When executing the command above with “-nstruct 1” Rosetta is sometimes able to complete successfully.

        Thanks in advance for any hint you may have!

      • May 28, 2021 at 3:56 pm #15910
        Anonymous

          From internal discussions, it sounds like recent versions of Rosetta have issues with TransformEnsemble — with exactly the symptoms you see. The first output structure works fine, but subsequent structures cause a crash.

          You may want to try running things with Rosetta 3.11 and see if that helps.

          • June 1, 2021 at 7:20 am #15912
            Anonymous

              Thank you very much for your quick response.

              Indeed, using Rosetta 3.11 the  RLE protocol worked.

              Nonetheless, we still had to modify slightly the example input files distributed with the source code, in particular removing the keyword “optimize_until_ideal”, to get rid the error message:

              Error: Element ‘TransformEnsemble’, attribute ‘optimize_until_ideal’: The attribute ‘optimize_until_ideal’ is not allowed.

              Since we couldn’t find the documentation for this option, I would like to ask whether you could point us to the right resource to look it up  or briefly explain what this option is supposed to do? (so we could understand whether omitting it is fine or not)

              Thanks in advance for your feedback!

          • August 26, 2021 at 5:16 pm #15998
            Anonymous

              Has a solution been found for issue described above? I am using Rosetta 3.13 and having this same issue when I run the demo for RLE (/PATH/TO/ROSETTA/main/demos/protocol_capture/rosettaligand_ensemble/):

              Error: Element ‘TransformEnsemble’, attribute ‘optimize_until_ideal’: The attribute ‘optimize_until_ideal’ is not allowed.

              When I delete optimize_until_ideal=”true” from the dock. xml file, RLE will run. However, it only works with nstruct = 1. Otherwise, I get a segmentation fault. 

              Any help would be much appreciated. Thanks!

               

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