Translate mover chain X doesnot exist.

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    • July 9, 2020 at 3:36 pm #3501
      Anonymous

        Hi all,

                  we are trying to run protien -ligand docking. We were able todo succesfully the tutorial and do for some of our drug molecules except “Diltiazem”. we generated conformers using online tool [mentioned in the tutorial] and tried schrodinger conformers too. but the following error still persists. Screen shot is attached.

        ‘Translate’ mover” chain X doesnot exist.

        We checked the conformers pdb file every conformer is seperated by ‘TER’ text and both PDB and conformers file has chain X.

        we are in the process of manuscript revision with tight timeline and we are struck with this issue.

         

      • July 9, 2020 at 3:48 pm #15378
        Anonymous

          The Translate mover isn’t looking for chain X in the conformers file, it’s looking for it in the input structure. (Roughly, what you’ve passed to -s)

          The RosettaLigand movers assume that you already have some sort of starting complex of protein+ligand. RosettaLigand isn’t a global pocket search – it assumes you already know roughly where the ligand should be, and have started the ligand off where it should go. The StartFrom mover that you have won’t put the ligand into the structure, it will assume the ligand is already there, just in the wrong position. (It also won’t complain if the ligand is missing.)

          I’d double check your Diltiazem input files, and make sure that the Diltiazem ligand is present in your input and is listed as chain X in the PDB file you’re passing to -s.

          • July 9, 2020 at 4:27 pm #15379
            Anonymous

              Attached are the input file, we used…

            • July 9, 2020 at 5:37 pm #15388
              Anonymous

                Everything looks to be in order, as far as I can tell.

                Could you send me the full set of input files (including the XML) and the command line you used? Perhaps if I can run it on my local machine I can figure out what’s happening.

              • July 10, 2020 at 5:25 pm #15398
                Anonymous

                  Atatched is the xml script as .log extension .

                • July 10, 2020 at 5:28 pm #15394
                  Anonymous

                    module load rosetta/3.8

                    /home/tfeng/rosetta_bin_linux_2018.33.60351_bundle/main/source/bin/rosetta_scripts.static.linuxgccrelease @options.txt -nstruct 500 -database /home/tfeng/rosetta_bin_linux_2018.33.60351_bundle/main/database/

                     

                • July 14, 2020 at 5:54 pm #15406
                  Anonymous
                    It looks like the issue was flagged in the mess of Warning messages which got printed out:
                     

                    core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] skipping pdb residue b/c it’s missing too many mainchain atoms:    1 X DIL DILE:CtermProteinFull:NtermProteinFull

                     
                    So DIL is the name which Rosetta uses for D-isoleucine. It looks like the PDB reader is getting confused about what residue the “DIL” entry in the input PDB is supposed to be. For some reason it’s thinking it’s supposed to be the D amino acid, as opposed to your passed parameter, then throwing up its hands when it can’t find the atoms it expects.
                     
                    The quick fix would be to simply change the three letter code used for this ligand. That is, change the line in the params file to be something like `IO_STRING XIL Z` and then change the three letter code in the DIL.pdb file to also be XIL.  (There’s no particular reason for XIL — you just want to pick something that Rosetta won’t confuse for another residue.)
                     

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