AMBER Archive (2008)

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

From: prateeksha s (prateeksha.s_at_gmail.com)
Date: Thu Apr 10 2008 - 01:11:35 CDT

Dear All,

To get charges for the protonated adenine, I followed methods
described in *AMBER
Force Field Parameters for the Naturally
Occurring Modified Nucleosides in RNA - Aduri et al* .

I split my molecule into 3 parts. Ran *g03* on the *com* files. So, I have 3
*log *files from the run - which I assume are the *gout *files. The next
step is to run *antechamber* with *resp* option on them to get the charges.
But somehow its going wrong, its not recognizing the **.ac* file produced
the first time *antechamber* is run.

The set of commands I use while running *antechamber *are similar to:
* antechamber -fi pdb -fo ac -i input.pdb -o input.ac -c mul
am1bcc -i input.ac -f ac -o input.ac -j 4
atomtype -i input.ac -o input.ac -p gff
prepgen -i input.ac -f prepi -output.prepi
*
Thanks,
Prateeksha

On Fri, Mar 21, 2008 at 10:02 PM, prateeksha s <prateeksha.s_at_gmail.com>
wrote:

> 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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>
>

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