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forlilab / waterkit

Tool to predict water molecules placement and energy in ligand binding sites
GNU General Public License v3.0
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run_waterkit.py failed #4

Closed xiedq closed 10 months ago

xiedq commented 1 year ago

We tried to use waterkit to predict the distribution of water molecules near the binding site of protein-small molecule complex, but if the small molecule contains Cl atoms, when run the step run_waterkit.py, an error occurred.

run_waterkit.py -i com_prepared_amber.pdbqt -c 26.95 6.16 4.15 -s 23 23 23 -n 10000 -j 16 -o traj

PDBQT parsing error: Atom type CL is not a valid AutoDock type (atom types are case-sensitive).

ATOM 2610 Cl1 BNZ A 163 29.032 7.968 2.789 1.00 1.00 -0.097 CL

in our input amber_pdbqt file: ATOM 2611 Cl1 BNZ A 163 29.032 7.968 2.789 1.00 1.00 -0.097 cl

com_prepared_amber.zip

jeeberhardt commented 1 year ago

Hi,

Thanks for the feedback! The issue is fixed now (add19c52b4b1baf31b7fa44067fca3d6d17f6402).

Best, Jerome.