RE: AMBER: perturbed atoms are not bonded on using TIP5P water

From: sugino tatsuro <>
Date: Fri, 12 Jan 2007 22:58:40 +0900


Thanks for your quick reply very much.

I created my system such that 1293 TIP5P waters were placed around a water
molecule by using xLaep. Then I chose one of the water molecules to be
Only electric charge of atoms of the water molecule was perturbed into 0
from default value.
Bond information of perturbed water molecule could be confirmed by the
command "desc" before saving topology and coordinate files.
But there was no bond information in the saved topology file.
So,when I performed MD simulation with these saved topology and coordinate
files, perturbed atoms moved separately (because these are no bond).

Thank you, with regards

-----Original Message-----
From: [] On Behalf Of
David A. Case
Sent: Friday, January 12, 2007 7:12 AM
Subject: Re: AMBER: perturbed atoms are not bonded on using TIP5P water

>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
>> of the waters.
>> I successfully generated topology and coordinate files. But, in the
>> 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
>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?


>The AMBER Mail Reflector
>To post, send mail to
>To unsubscribe, send "unsubscribe amber" to

The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to
Received on Sun Jan 14 2007 - 06:07:47 PST
Custom Search