AMBER: Amber 8: create topology for solvent - PBC box size problem

From: Angela Liu <>
Date: Wed, 13 Jul 2005 11:41:04 -0700 (PDT)

Dear Amber users,

I was trying to create a topology file for only the
solvent molecules in a truncated octahedron. I used
the method posted by Thomas E. Cheatham, III on Mar 16
but I couldn't maintain the same box dimension as the
original topology file. There are a few other odd
things that I noticed as well.

As a test, I first used tleap (FF03) to solvate a PDB
structure in truncated octahedron and saved its
topology file ("initial.prmtop") and structure
("initial.pdb"). Then I used tleap to load this
"initial.pdb" back and added periodic boundary
information using the command "solvateoct". TIP3PBOX
was used for both. I was hoping this would generate
an identical .prmtop file as "initial.prmtop".

However, when I used a zero buffer and a large
closeness for "solvateoct" as Cheatham suggested, the
new box is larger in dimension than the original
"initial.prmtop". The number of water molecules
stayed the same. What range of values can be used for
buffer and closeness so that the same box size is

My tleap script looks something like the following:

> model = loadpdb "initial.pdb"
> check model
> solvateoct model TIP3PBOX 0.0 100.0
> savepdb model recreated_box.pdb
> saveamberparm model recreated_box.prmtop

Below is the excerpt of Cheatham's approach:

> p.s. if you are having trouble with xleap crashing,
try tleap; it should
> easily work to build the new prmtop based on reading
of a PDB file.
> In your case, if you are stripping the solute (i.e.
:1-25) and building
> a prmtop for just the solvent in a truncated
octahedral geometry,
> you will need to load the pdb and then build the box
> this is normally done with the setbox command,
however this will
> not work for truncated octahedron. For this, you
need to play with
> solvateOct setting a small buffer and large
closeness so that a box is
> built, but no water is added.

Two other things that are different in the new
topology file are:
1) the RADII section for H2 in WAT is 1.2 instead of
2) the BOND_INC_HYDROGEN section contains many
permutations of the bonds.
But single-point energy calculations show that these
two differences do not affect the potential energy.

One more thing I have observed is the new files
generated by the tleap script above,
"recreated_box.pdb" and "recreated_box.inpcrd", show
very different 3-D coordinates. This seems very
strange consider the "model" tleap used to save them
is the same. When VMD is used to view these two
structures, a translation-rotation is required to
superimpose these two sets of coordinates. I wonder
why these two files do not share the same coordinates.

Thank you very much for your help!

Best wishes,

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Received on Wed Jul 13 2005 - 19:53:00 PDT
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