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
conditions
%J J. Chem. Phys.
%V 109
%P 10921-10935
%D 1998
...dac
--
==================================================================
David A. Case | e-mail: case_at_scripps.edu
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 | http://www.scripps.edu/case
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Received on Fri Aug 02 2002 - 22:16:18 PDT
