I am trying to relax my structure which contains a bound ligand.
First, I created a LG.params file using:
python /path/to/molfile_to_params.py /path/to/1XKK_ligand.mol2
This file (1xKK_ligand.mol2) only contains the coordinates for the ligand from the PDB 1XKK. molfile_to_params.py outputs the LG.params file as well as a PDB, which looks correct when visualy inspected. This is all expected.
Then I am running the relax application with the following command:
-database $ROSETTA_DATABASE \
-s /path/to/1XKK.clean.pdb \
-native /path/to/1XKK.clean.pdb \
-out:file:silent 1XKK.relaxed.a.out \
-nstruct 1 \
-out:file:scorefile 1XKK.relaxed.a.score.csv \
-extra_res_fa /path/to/FMM.params \
-relax:ramp_constraints false \
-no_optH false \
This command executes ok, but when I look at the final PDB after extracting it from the silent output file, I see that the coordinates for the ligand are completely messed up. The side chains for the protein itself look ok (not shown in the images below).
Here are what the CORRECT (before relax) ligand looks like:
And here is what the INCORRECT (after relax) ligand looke like:
Does anyone have any idea why this is happening???