Re: water box-nonperiodic

From: David Case <>
Date: Fri 2 Aug 2002 22:16:18 -0700

On Fri, Aug 02, 2002, Cozmuta wrote:
> I am trying to build a water box with one single ion (K, Cl or Na) in the
> center. I am loading the TIP4P model box and use the addIons command to
> add the one ion. I get the following message:
> addIons ttt K+ 1
> K+ has a charge of 0.
> Adding the ions anyway.
> Adding 1 counter ions to "ttt" using 1A grid
> addIons: No solute to add ions to
> When I edit the structure the ion is not in the water box.
> What is the correct way to build this?

Try this:

solvateBox K+ TIP4PBOX <size-of-box/2> ...
saveAmberParm K+ ....

This makes the ion the "solute".

> Is there an equivalent way in AMBER
> to the MMFP module in Charmm (not to run PBC but impose restraint
> potentials on the water molecules so that they do not escape from the
> "box")?

I don't know this CHARMM command, but from your description, it doesn't
sound like it; you could use a spherical "droplet" without PBC, but I
don't know why you would want to do that. See:

%A T. Darden
%A D. Pearlman
%A L.G. Pedersen
%T Ionic charging free energies: Spherical versus periodic boundary
%J J. Chem. Phys.
%V 109
%P 10921-10935
%D 1998


David A. Case                     |  e-mail:
Dept. of Molecular Biology, TPC15 |  fax:          +1-858-784-8896
The Scripps Research Institute    |  phone:        +1-858-784-9768
10550 N. Torrey Pines Rd.         |  home page:                   
La Jolla CA 92037  USA            |
Received on Fri Aug 02 2002 - 22:16:18 PDT
Custom Search