Re: AMBER: Solvate box

From: M. L. Dodson <>
Date: Tue, 13 Feb 2007 21:33:49 -0600

In addition to the suggestions made by Ross, you might want to
look at packmol (
This program can generate a starting system for MD with quite a
bit of complexity. One of the examples is a box containing the t3
hormone at the interface of chloroform and water (generated in 9
seconds for a system of 1219 molecules and 4087 atoms). The
minimum distance between solvent molecules can be specified as
well as the box (or, e.g., sphere) dimensions.

The user guide is available on the web site as is an interactive,
web-based "volume guesser" for estimating the volume needed to
achieve a specified density given the solvent and solute

One of the nice things is that you can explicitly specify the
number of solvent molecules to be used. This problem has come up
several times in the last few months, although I do not think
packmol would be a general solution. There is no correspondence
between the solvent molecule order when two boxes are generated
with slightly differing solutes.

I've not used the program "for real", but I have played around
with it, and it seems quite capable of doing what is described.

Bud Dodson

On Tuesday 13 February 2007 10:26, Ross Walker wrote:
> Dear Sophie,
> > I want to simulate a molecular dynamic simulation of a
> > protein into Water/Octan
> > interface (explicit solvent). Therefore, I want to use two
> > boxes : a cubic
> > water box and a octane box. The major part of the protein
> > must be in the water
> > box. One part of the protein must be in the octan box. So, I
> > have to put the
> > octane box on the water box.
> > I don't know how I can use two boxes and put one box on the other box.
> This is a complicated problem and you are going to have to do quite a bit
> of manual work. I would anticipate around a days work or so.
> I would start by making sure you can build or acquire a box of octane
> solvent and that it equilibrates to the correct density etc. Next I would
> try and create a box containing water and octane. Run some simulations of
> this to verify the properties,do you see the correct interface / mixing
> properties etc. Once you have verified this you can then try to build you
> solvated protein. This is the tricky bit and will take some work on your
> part. I can think of a number of ways to approach this and some might be
> easier than others. One would be to create the water octane box at the
> size you need. Probably the best way to do this is to build a large box
> of water and a seperate large box of octane, write pdbs of both and then
> cut them down to the sizes you need. Then cat the two pdbs together. This
> gives you your mixed solvent box. You should probably then equilibrate
> this and at the end convert the restart file to a pdb. Then create the
> necessary transformation matrix to orient your protein correctly with the
> axis of the box and the interface. Next translate the coordinates of you
> protein so it matches the solvent box. I would then append the solvent
> box to the end of the pdb. Next you will need to write a script that goes
> through each solvent molecule in the box and calculates if any are
> overlapping or to close to the solute. You may have to play about with
> the optimum distances here. If it finds an atom too close or overlapping
> your script should then delete the solvent molecule. At the conclusion of
> this process you should have a pdb of your protein in the solvent as you
> desire. You can then load this into leap with the necessary parameters
> and use the setbox command to create the bounding box and set the prmtop
> periodicity flag. Then save your prmtop and inpcrd file and you should be
> all set.
> There may be a simpler way to do this but I don't know of any automated
> tools for doing it.
> All the best
> Ross

M. L. Dodson
Email:	mldodson-at-houston-dot-rr-dot-com
Phone:	eight_three_two-five_63-386_one
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Received on Wed Feb 14 2007 - 06:07:48 PST
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