Re: equilibrated solvent box

From: David A. Case <>
Date: Wed 22 Jan 2003 08:48:12 -0800

On Mon, Jan 20, 2003, pu xuemei wrote:

> solvatebox enzyme HEXA 10.0 (HEXA is variable name of hexa.lib)

> so I want to add more hexane molecules on condition of no increasing box
> size too much ( I afraid that too large boxsize lead to simulation died).I
> use smaller closeness than 1 angstrom in solvating, but which can not add
> enough hexane( up to 1000 molecule at most).

You need to increase the cutoff distance (10.0 above) if you want more
solvent molecules. There is no real way go get more solvent without
increasing the box size. It is probably also a good idea to add a closeness
parameter of something like 0.7 to 0.8 (this is dimensionless, not Ang.)

> Maybe one equilibrated hexane solvent box can be one solution to the
> problem. In order to get one equilibrated solvent box, I do so in xleap as
> follows:
> solvatebox HEXA HEXA 10.0 (using hexane as solute and solvent)
> saveamber HEXA prmtop inpcrd
> then equilibrate the solvent box in constant pressure.But I don't know how
> to do next step,in other words, how I convert the restart or trajectory
> file to parameters file (like WATBOX216) so that I could solvate enzyme
> using the equilibrated solvent box in continuing work.

Use ambpdb to convert the coordinates to pdb format, then read it back into
LEaP and use the "setBox" command to make it periodic. Save it as on off
file. (Optional, but recommended: manually edit the off file to make sure
the box size matches that at the bottom of your final equilibrated restrt

..good luck...dac

David A. Case                     |  e-mail:
Dept. of Molecular Biology, TPC15 |  fax:          +1-858-784-8896
The Scripps Research Institute    |  phone:        +1-858-784-9768
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Received on Wed Jan 22 2003 - 08:48:12 PST
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