If you just leave them as found and named in the pdb file it should work
fine (if it's from RCSB). If it doesn't work, share the leap.log so we can
see what leap did.
On Thu, Mar 10, 2022, 7:06 PM Daniel Konstantinovsky <
daniel.konstantinovsky.yale.edu> wrote:
> 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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>
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Received on Thu Mar 10 2022 - 16:30:03 PST
