RE: AMBER: Solvate box

From: Ross Walker <>
Date: Tue, 13 Feb 2007 08:26:51 -0800

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

|\oss Walker

| HPC Consultant and Staff Scientist |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- |
| | PGP Key available on request |

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Received on Wed Feb 14 2007 - 06:07:41 PST
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