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 - 01:19:40 CDT

oops! I realized I skipped the convert gjf to pdb part !
for that I need gjf2pdb.exe . I searched the net and can't find it. Can
anyone let me know where I can lay my hands on it ?

rgds
prateeksha

On Thu, Apr 10, 2008 at 11:41 AM, prateeksha s <prateeksha.s_at_gmail.com>
wrote:

> 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
> > >
> > >
> > >
> > > -----------------------------------------------------------------------
> > > The AMBER Mail Reflector
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> > >
> >
> >
>

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