On Thu, Mar 10, 2022, Daniel Konstantinovsky wrote:
>
>I want to use tleap to solvate a protein but I want to keep the
>crystallographic water molecules in place as regular solvent but with their
>initial positions. I have added hydrogens to these waters and made them
>TIP4P by adding an EPW dummy atom. I checked and it seems tleap strips the
>water molecules off the structure....
This is unlikely: tleap doesn't remove waters (or anything else). There
should be no need to add hydrogens or add dummy atoms: if they are called
HOH or WAT, they should get recognized, and whatever force field you
requested in your leaprc.water.xxxx will be applied. (You might try
renaming the crystallographic waters as WAT, but I don't think(?) that
should be needed.)
Look carefully at the leap.log file for any clues about what is happening.
You might post the relevant parts of the PDB file, and the tleap commands to
you are using.
...good luck...dac
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Received on Thu Mar 10 2022 - 18:00:02 PST
