AMBER Archive (2004)

Subject: Re: AMBER: xleap solvatebox problem

From: David A. Case (
Date: Thu May 27 2004 - 10:42:48 CDT

On Thu, May 27, 2004, Tomas Kubar wrote:
> I have been trying to simulate the system of two methane molecules
> dissolved in a box of TIP3P water. To build this system, I attempted to
> use the xleap program from the AMBER 8 package. A problem occured when I
> wanted to solvate the two methanes:
> > solvatebox CH4 TIP3PBOX 10
> The program created a box and filled it with water, but the resulting
> density was 2.2 g/cc. An attempt to equilibrate such a system led to an
> error - excessive number of nonbonded pairs.

Works for me, unless there is something unusual about your CH4 unit. I
tried the following:

Welcome to LEaP!
(no leaprc in search path)
> source leaprc.ff94
> solvatebox ACE TIP3PBOX 10
  Solute vdw bounding box: 6.053 5.036 4.754
  Total bounding box for atom centers: 26.053 25.036 24.754
  Solvent unit box: 18.774 18.774 18.774
  Total vdw box size: 28.912 28.370 27.815 angstroms.
  Volume: 22814.792 A^3
  Total mass 8402.468 amu, Density 0.612 g/cc
  Added 464 residues.

You could try the above, just in case there is some special about your CH4
unit. Other than that, I don't have any ideas about what might be going on.
You could compare the box size and number of waters you get with numbers like
those shown above; maybe that would provide some clue.



================================================================== David A. Case | e-mail: Dept. of Molecular Biology, TPC15 | fax: +1-858-784-8896 The Scripps Research Institute | phone: +1-858-784-9768 10550 N. Torrey Pines Rd. | home page: La Jolla CA 92037 USA | ================================================================== ----------------------------------------------------------------------- The AMBER Mail Reflector To post, send mail to To unsubscribe, send "unsubscribe amber" to