AMBER Archive (2004)

Subject: AMBER: xleap solvatebox problem

From: Tomas Kubar (tomas.kubar_at_uochb.cas.cz)
Date: Thu May 27 2004 - 07:33:44 CDT

Hi all

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.

With xleap verison 7, the solvation ran OK (resulting in density of 0.6
g/cc).

May this be a bug in leap, or have I been doing something wrong?

thanks

tom
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