AMBER Archive (2008)

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

From: prateeksha s (prateeksha.s_at_gmail.com)
Date: Fri Mar 21 2008 - 11:32:06 CDT

Thanks will do that and get back.

rgds,
Prateeksha

On Fri, Mar 21, 2008 at 1:13 PM, FyD <fyd_at_q4md-forcefieldtools.org> wrote:

> 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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