AMBER Archive (2008)

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

Date: Fri Mar 21 2008 - 10:29:18 CDT

Dear Prateeksha,

You need to generate a new residue for the protonated Adenosine. Once you have
the force field files for this residue, you can use it along with the usual ff
to carry out your simulations. You can find a detailed description of how to
generate "prepin" and "frcmod" files for a modified nucleoside in the following
"Aduri, al., J. Chem. Theory Comput., vol. 3, 1464 - 1475, 2007"
I hope this helps.

Raviprasad Aduri

Quoting prateeksha s <>:

> Hi,
> I want to simulate protonated adenine. So which charge scheme one should use
> for that?
> 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.
> Please give your inputs.
> Thanks and cheers,
> Prateeksha

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