Re: Xtal Waters and SolvateBox

From: Bill Ross <>
Date: Tue 24 Oct 2000 13:58:17 -0700 (PDT)

        I want to create with xLEAP a solvateBox around a protein that
        has 600 water molecules in the crystal structure (1b6g), and I
        want to keep the water of the crystal.
        How can I do that?

They need to have residue and atom names matching WAT, which
it appears that you have done, since .top & .crd were obtained:

        I have tried several times and xLEAP is not properly handeling
        the waters of the crystal.
        There is some problem in the .top and .crd files obtained after
        using the "solvateBox" command, because when I later run energy
        minimization with SANDER, the energy given is out of scale (too big).
        But if I delete the waters of the crystal everything works fine.
I bet that the xtal waters have one or more of these problems:

 - lack H coordinates & default ones applied have steric problems
 - O's are poorly placed sterically
 - are not in the proper pdb format so that coordinates are misread

If the vdw is out of scale, I suspect placement of O's, if electrostatic,
I suspect missing H's.

To check HW placement, look with xleap before solvating.

Bill Ross
Received on Tue Oct 24 2000 - 13:58:17 PDT
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