AMBER Archive (2008)

Subject: Re: AMBER: Charge scheme for simulating protonated adenine

From: FyD (fyd_at_q4md-forcefieldtools.org)
Date: Fri Mar 21 2008 - 02:43:51 CDT

Quoting prateeksha s <prateeksha.s_at_gmail.com>:

> 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 @
http://q4md-forcefieldtools.org/Tutorial/Tutorial-1.php#14
See "Scheme 4" in particular.

You will find examples of new nucleic acid fragments in R.E.DD.B. @
http://q4md-forcefieldtools.org/REDDB/up/F-59/
or
http://q4md-forcefieldtools.org/REDDB/up/F-58/

> 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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