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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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Placing water with predicted .dx files only? #19

Open johnnytam100 opened 4 weeks ago

johnnytam100 commented 4 weeks ago

Hi, I would like to use waterkit to perform explicit water placement with predicted .dx files (from other algorithms) without performing any MD simulations. Can waterkit do that?

rwxayheee commented 4 weeks ago

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

rwxayheee commented 4 weeks ago

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 :>