AMBER Archive (2008)

Subject: Re: AMBER: How to extract solvent box information from .rst or .mdcrd files?

From: David A. Case (
Date: Sat Jun 28 2008 - 11:37:45 CDT

On Thu, Jun 19, 2008, Panwang Zhou wrote:
> I'm trying to build a DMF solvent box using the gaff force filed. The
> initial solvent box was built using the xleap, then the MD studies were
> performed to equilibrate the solvent box. After equilibrium, the density of
> the solvent box was about 0.976 g/cc, which seems to be in accord with the
> experimental value (0.9445g/cc). The other properties I have not checked.
> Can anyone tell me how to extract the final solvent box from the obtained
> .rst or .mdcrd files? I want to obtain the "off" file which can be directly
> loaded by xleap.

You may have to play a bit, since I don't know that this procedure is
explicitly documented anywhere. Try this:

1. use ptraj to image your coordinates back into the primary box. Save as a
pdb file.

2. Use leap to load the pdb, set the box size manually (this is at the bottom
of the rst file), then save the unit as an off file.

3. Compare what you have to something like the "" file in the
$AMBERHOME/dat/leap/lib directory. Use a text editor to make any changes
needed, so that your file has the same information as in the file.

...good luck....dac

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