Re: POL3

From: Bill Ross <>
Date: Mon 30 Oct 2000 14:25:06 -0800 (PST)

                I would like to use the POL3 water polarizable potential
                with Amber5. How can I build a box with POL3 water
                molecules using leap ?
                Which file contains the parameters for POL3 molecules ?
        I hear that POL3 uses a rigid water model, so the parameters
        for the provided TIP3 water can simply be modified by loading
        a frcmod file redefining whatever is needed for the water atom
        types, OW and HW.

Oops, that is assuming that the atomic charges are the same as
in TIP3 as well. If the charges are different, it might be as well
to build a separate water model.

The methane tutorial on the amber web illustrates how to
build a new molecule; don't forget to add an H-H bond for
rigidity. In this case you would again put the parameters
in a frcmod file. Then you could solvate the new molecule
with itself to get a starting box:

> x = copy POL
> solvatebox x POL 10
> saveamberparm x polbox.crd

This you would equilibrate in sander (e.g. by running at 300K
constant volume until energy levels off, then shifting to
constant pressure until volume levels off). This model would
be converted to pdb (ambpdb, pdbgen or carnal), loaded into
leap, box added, and saved as a unit:

> POLBOX = loadpdb polbox.pdb
> setbox POLBOX
> saveoff POLBOX polbox.lib

Bill Ross
Received on Mon Oct 30 2000 - 14:25:06 PST
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