I think all that is happening is that tleap translates the system to a new
center. I have confirmed that the original waters are still there by
aligning to the original structure. I'm just writing this for future people
who have this problem so they see that it's ok.
On Thu, Mar 10, 2022 at 8:37 PM David A Case <david.case.rutgers.edu> wrote:
> 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 Fri Mar 11 2022 - 07:30:03 PST
