I am relatively new to Rosetta and have been trying to get my head around RosettaLigand. I have run into a problem with the pdb files that I get out from a run.
In some instances when I run the Rosetta ligand docking, the pdb files that come out for each run show the ligand docked in a logical position. However, the ligand itself is modified to display extra bonds between some atoms that were not in the input/native pdb files.
Is there any way that I can stop this from happening?
Thanks very much.
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Problems with ligand when running RosettaLigand