Complex protein ligand Issue

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Hello everyone,

I would like to ask if the following behavior is normal when building a ligand-protein complex in GROMACS. I am following the standard procedure:

  1. I run the command gmx pdb2gmx -f PRO.pdb -o PRO_processed.gro for the protein ( charmm36 ff).
  2. Then, for the ligand, I use gmx editconf -f LIG.pdb -o LIG.gro.

After that, I form the ligand-protein complex by adding the specific content of LIG.gro into PRO_processed.gro. However, when I visualize the result (complex.gro), I get an unexpected image.

In other tests I’ve performed with the same protein and two different ligands, one ligand sits directly in the protein while the other is positioned at a relatively long distance.

Here are the file contents and the image: Attach File and image
Thanks

2

To avoid other people answering in this thread, I think this issue was resolved (as one of the issues) in Error Coordinat not matching gromacs.

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