Re: [AMBER] solvatebox

From: <>
Date: Tue, 7 Dec 2010 13:25:41 -0500 (EST)

It's probably not possible to have all of the conditions that you have
specified. There's no way to guarantee that a cubic box of dimension 62A
will enclose your protein by 8A unless the maximum distance between any
two atoms in your protein is less than 46A, obviously. But, I think that
having the box enclose the protein by a particular minimum distance is by
far the most important of the criteria you have mentioned. In order to
ensure that this is the case throughout the simulation, you will need to
do two things.

First, use a command such as:

solvatebox <nameofyourstructure> TIP3PBOX 9.0

Notice that I have inflated the minimum distance. This is because, after
equilibration, the molecules in your system will settle like any granular
substance and the box will shrink. It's advisable to have the minimum
distance between the protein and the box boundary be at least the nonboded
cutoff (that is, the Lennard-Jones cutoff--electrostatics will likely
pertain to the infinite system if you're running in AMBER) PLUS a little
extra, perhaps half the width of a solvent molecule, so the distance you
need to use may even be larger than 9A. The general idea is that the same
image of one molecule should not influence two images of another molecule
simultaneously, nor vice-versa (I will venture, if your system is as large
as a solvated protein it would be hard to quantify any such artifacts--but
even then you certainly don't want the protein adversely influencing

The second thing you will have to do is edit the final line of the
coordinates file produced by LEAP, so that the first three numbers are all
equal. To avoid any clashes, just set them all to the largest box
dimension plus 1-2 Angstroms. This will create a vacuum around the
system, but it will equilibrate quickly if a barostat is applied (ntb = 2)
and the protein will not be adversely affected if restraints are in place
(ntr = 1, with an appropriate restraint mask) during equilibration. So
long as you use isotropic position rescaling (ntp = 1), the simulation
cell will remain cubic, forever.

It is a good idea to have your box be cubic, rather than a shoebox, if you
are doing truly equilibrium dynamics. The rate at which proteins can
tumble in these simulations is actually quite high, I've observed, so you
can see rapid changes in the minimum distance between the protein and the
box boundaries (which is perhaps better stated as the minimum distance
between two images of the protein itself) in a few nanoseconds. This is
probably a good example of how multiple images of a protein can influence
one another artifactually, though the consequences of this diffusion are
probably not drastic and seldom measured. A cubic system guarantees,
after settling and volume equilibration, a minimum distance between two
protein images provided that the protein stays folded. In the other
extreme, a straight DNA helix placed in a tall skinny box might rapidly
have its images come into close contact; a simple model of the DNA as a
uniformly charged cylinder would obviously not have such problems, but all
of these systems are going to have asymmetries, in addition to local
fluctuations, that cause them (mostly via long-ranged electrostatics) to
tumble more rapidly than something like the Stokes equation would suggest.
 Therefore, cubes and truncated octahedra are the unit cells of choice for
solution phase simulations of any significant length.


> Dear Leila,
> With the information you have provided, you might want to try PACKMOL -
> Starting with a pdb for a water molecule and the pdb of your solute, you
> can
> easily define a PACKMOL input to prepare your system.
> Regards,
> Igor Marques
> On Tue, Dec 7, 2010 at 3:21 PM, Oliver Grant <>
> wrote:
>> in leap use this command:
>> solvatebox <nameofyourstructure> TIP3PBOX 8.0
>> Oliver
>> On 7 December 2010 12:00, leila karami <> wrote:
>> > Dear amber users
>> >
>> > I'm beginner in amber.
>> >
>> > I want to have a water box with following conditions:
>> >
>> > water model = TIP3P
>> > distance between the solute and wall of the box = 8 angstroms
>> > number of water molecules = 7400
>> > box type = cubic
>> > box length = 62 angstroms
>> >
>> > How I should use solvatebox for obtaining them?
>> > _______________________________________________
>> > AMBER mailing list
>> >
>> >
>> >
>> _______________________________________________
>> AMBER mailing list
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Received on Tue Dec 07 2010 - 10:30:04 PST
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