Docking with water molecules present

[peterk]

Dear Sargis,

Is it possible to keep the water molecules when preparing the docking protein using Autodock/ Make Macromolecule?
I'm using the 0.9-version.
It looks like the the water molecules are deleted when preparing the macromolecule.
Is there a way to keep the water molecules?

Thanks!
Peter

[sargis]

Dear Peter,

You can edit https://sourceforge.net/apps/trac/pyrx/ ... el.py#L358 and remove "_waters" from there (i.e. cleanup='nphs_lps_waters' => cleanup='nphs_lps' ) to keep the water molecules. Search for site-packages\PyRx to find where this file is located on your filesystem. Then (re)start PyRx for changes to take effect.

Thank you for using PyRx!
Sargis