AMBER Archive (2007)

Subject: Re: AMBER: perturbed atoms are not bonded on using TIP5P water

From: David A. Case (case_at_scripps.edu)
Date: Thu Jan 11 2007 - 16:12:23 CST

On Thu, Jan 11, 2007, sugino tatsuro wrote:
>
> 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.

We need to know more about how you created the perturbed water: what does it
become in the perturbed state? What happens to the extra points that were
originally on the TIP5P model. How did you go about doing this?

...dac

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