AMBER: perturbed atoms are not bonded on using TIP5P water

From: sugino tatsuro <>
Date: Thu, 11 Jan 2007 23:12:09 +0900


I have a problem in Amber 8.
I'm going to perform thermodynamic integration using TIP5P model.
The system I use is 3,000 water molecules, and the perturbed molecule is one
of the waters.
I successfully generated topology and coordinate files. But, in the topology
file, the perturbed atoms are not bonded with other atoms. Namely, oxygen
atom is not bonded with hydrogen atoms.
Such phenomenon does not occur when TIP3P is used.

Thanks for your help.


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Received on Sun Jan 14 2007 - 06:07:25 PST
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