AMBER Archive (2003)

Subject: AMBER: Re: methylphosphonate

From: A. Hungie (hungie01_at_hotmail.com)
Date: Tue Jul 15 2003 - 03:31:52 CDT

Thank you very much for all suggestions from Prof. David Case, Prof.
Cheatham, Dr. David Volk, and Piotr Cieplak.

Best Regards,
Hungie

> >
> > I am familiar only with MD simulation of unmodified DNA using Amber. I
>am
> > using Amber 6 and I would like to do simulation of DNA modified by
> > substituting one oxygen atom of phosphate group with methyl group,
>namely
> > methylphosphonate. Could you please suggest me as follow?
> > 1. How to replace O1P (or O2P) atom with CH3 group?
>
>Use the edit command in xleap to convert the oxygen to a CH3. Then save
>the unit under a new name.
>
> > 2. Is force field of methylphosphonate available in parm94.dat or
> > parm99.dat? (I don't know how to check). If not, does anyone have such
> > force field?
>
>I don't think these are available. You should be able to use antechamber
>to
>generate the parameters, but that requires Amber 7.
>
>..good luck...dac

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