Running with --flexres give extremely high Energy

[BJWiley233]

Hi,

When I run my docking without --flexres it runs "as much" as expected and I'll get a some values like -11.34 kcal/mol or -10.21 kcal/mol for say two molecules. However when I add flex residues which I created with the below and run, I get all the same crazy high value for both (all) molecules.

pythonsh $TOOLS/mgltools_1.5.7_MacOS-X/MGLToolsPckgs/AutoDockTools/Utilities24/prepare_flexreceptor4.py -r protein.pdbqt -s protein:A:LEU16_GLU18_GLN20_ASP149_PHE15 -g protein_rigid.pdbqt -x protein_flex.pdbqt

pythonsh $TOOLS/mgltools_1.5.7_MacOS-X/MGLToolsPckgs/AutoDockTools/Utilities24/prepare_gpf4.py -r protein_rigid.pdbqt -x protein_flex.pdbqt -d iteration_1/docking/run -i sample.gpf -o protein_rigid.gpf

$TOOLS/MacOSX/autogrid4 -p 974769965.gpf

Generations |  Evaluations |     Threshold    |  Average energy of best 10%  | Samples |    Best energy
------------+--------------+------------------+------------------------------+---------+-------------------
          0 |          150 |16777216.00 kcal/mol |    0.00 +/-    0.00 kcal/mol |       0 |16777216.00 kcal/mol
          5 |        32759 |16777216.00 kcal/mol |    0.00 +/-    0.00 kcal/mol |       0 |16777216.00 kcal/mol
         10 |        64341 |16777216.00 kcal/mol |    0.00 +/-    0.00 kcal/mol |       0 |16777216.00 kcal/mol
         15 |        96646 |16777216.00 kcal/mol |    0.00 +/-    0.00 kcal/mol |       0 |16777216.00 kcal/mol
         20 |       128969 |16777216.00 kcal/mol |    0.00 +/-    0.00 kcal/mol |       0 |16777216.00 kcal/mol
------------+--------------+------------------+------------------------------+---------+-------------------

[BJWiley233]

ugh disregard, make grid map larger works. https://github.com/ccsb-scripps/AutoDock-GPU/issues/200 also going to try Meeko

[BJWiley233]

Well actually with some ligand with phosphates, make the grid maps larger still gives same energies.

[BJWiley233]

Hmm might be a problem with Meeko because the charges are all nan for this molecule.

[atillack]

Energies this large (>= 2^24 kcal/mol) typically mean that the ligand (or parts thereof) are outside the grid maps. This can be caused by maps that are too small but also by accessible areas that are too small (i.e. a box that is too far inside a receptor).