Comments (2)
rwxayheee
commented on August 11, 2024
Hi @johnnytam100
Not entirely sure if waterkit can do that (the dev team can tell you if it's supported or a future feature)
Outside of waterkit, MoFT is a utility tool in Amber to analyze volumetric (spatial density) data. The linked tutorial shows how to use it for water placements based on 3D-RISM density data. You can find the usage and technical details in a recent Amber manual
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rwxayheee
commented on August 11, 2024
Hi @johnnytam100
I would like to make a correction of my previous reply that waterkit is able to identify discrete hydration sites. The usage is explained in README
Let us know if you have any further questions :>
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Related Issues (18)
- Installation issues HOT 8
- ad_map attribute HOT 1
- wk_prepare_receptor.py failed HOT 2
- run_waterkit.py failed HOT 1
- Issue creating pdbqt file with ligand bound system HOT 13
- Is Waterkit suitable for ligand bound system? HOT 4
- How to calculate the dG, dH, dS and density all the hydration sites? HOT 2
- cutoff of desolvation free energy for a favorable hydration site? HOT 2
- use in docking or virtual screening
- Receptor preparation
- python 3.12 breaks waterkit HOT 1
- failed steps in receptor preparation; documentation on receptor prep? HOT 2
- wk_minimize_trajectory.py fails: kcal not accepted unit by openmm HOT 4
- Receptor preparation falied HOT 1
- numpy bool call throws exception for identification of hydration sites HOT 1
- documentation on output files from waterkit HOT 2
- Working directly with parm7 and coordinate files HOT 8
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