Re: AMBER: Charge scheme for simulating protonated adenine

From: FyD <>
Date: Fri, 21 Mar 2008 08:43:51 +0100

Quoting prateeksha s <>:

> I want to simulate protonated adenine. So which charge scheme one should use
> for that?

You need to generate your own library to the Tripos or OFF (or prep)
format for your molecule. I guess you even need to generate a new
library for a molecule fragment (compatible with fragments already
available) and not for the molecule itself.

To generate a new molecule fragment see first the following article:
Cieplak et al. J. Comput. Chem., 1995, 16, 1357-1377

Then, you can generate the fragment you are interested in following a
strategy described .
See "Scheme 4" in particular.

You will find examples of new nucleic acid fragments in R.E.DD.B. .

> Also, I'm having troubles with xleap displaying the protonated adenine. The
> un-protonated adenine displays fine. But, the Hs in protonated adenine are
> not getting recognized.

This is normal because your molecule is not recognized by LEaP. You
need to create your own library.

regards, Francois

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Received on Fri Apr 18 2008 - 21:12:48 PDT
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