error in mol2 to params conversion for GAliganddocking

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    • April 22, 2020 at 1:08 pm #3400
      Anonymous

        Hi I am trying to convert a mol2 file to params file using mol2genparams.py script. The mol2params conversion appears to work (please see attached log file) but when I run rosetta_scripts to perform GAliganddocking, it throws up an error “dont add residue bonds more than once”. I have looked at the params file but can’t see any obvious duplications. I am following the protocol outlined for generating mol2 file for GAliganddocking at this location. https://www.rosettacommons.org/docs/latest/GALigandDock-Preprocessing

        The .params file is uploaded as a txt file. I would deeply appreciate any help. I have been at it for a long time now and just can’t seem to find a work around. I have tried to generate mol2 file from different sources, also tried starting from SMILES, pdb and mol but ended up with the same result.

      • April 22, 2020 at 3:05 pm #15252
        Anonymous

          I think the issue may be the atom naming conventions in your mol2 file. It looks like you may have multiple atoms all named the same in the file, which causes the mol2genparams.py script to output multiple atoms with all the same name in the params file, which causes issues later on.

          I’d recommend using a (non-Rosetta) tool to assign unique atom names to each of the atoms in the mol2 file, and seeing if that fixes things.

        • April 23, 2020 at 12:19 pm #15253
          Anonymous

            That worked. Thanks!

            mol2 file before

            @<TRIPOS>ATOM

                  1 C           -5.7358   -2.2409    0.9286 C.3       1 LIG1   -0.2041

                  2 C          -5.8896   -0.8952    0.2679 C.2       1 LIG1    0.5851

                  3 O          -6.9164   -0.6204   -0.3170 O.2       1 LIG1   -0.6291

            mol2 file after

            @<TRIPOS>ATOM

                  1 C1           -5.7358   -2.2409    0.9286 C.3       1 LIG1   -0.2041

                  2 C2         -5.8896   -0.8952    0.2679 C.2       1 LIG1    0.5851

                  3 O3         -6.9164   -0.6204   -0.3170 O.2       1 LIG1   -0.6291

            Note that the second column in the mol2 file now contains atom numbers. I basically opened my mol2 file in Chimera, loaded atom labels using 

            Actions -> Label -> Other -> serial number and edited the atom name by opening the mol2 in a separate text editor. 

             

            Thanks again for the help, 

            abhishek

             

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