You can use Leap in Amber Tools to create the topology files. Take a look at
the Amber Tools manual.
--------------------------------------------------
From: "fancy2012" <fancy2012.yeah.net>
Sent: Tuesday, April 13, 2010 8:29 AM
To: "AMBER Mailing List" <amber.ambermd.org>
Subject: [AMBER] How to prepare the two tolopogy files when doing
TIcalculation?
> Dear amber users,
> I want to do some TI calculation using GMX, and I have learned how to run
> it from the web tutorial. But there is still a problem. I don't know how
> to prepare the two topology files, which are initial and final states,
> respectively. For example, molecule A to molecule B, while the two
> molecules have only one different functional groups.
>
> Could somebody give me some suggestion on it? Any response will be highly
> appreciated! Thanks!
>
> All the best,
> fancy
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Received on Tue Apr 13 2010 - 06:00:03 PDT
