Hello Amber,
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 before/while solvating because none of
the new water molecules have the coordinates of any of the original waters.
Some of the water molecules are in hidden pockets of the protein that the
solvent would never penetrate in a reasonable amount of time. What can I do?
Thank you!
Dan
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Received on Thu Mar 10 2022 - 16:30:02 PST
