AMBER Archive (2003)

Subject: AMBER: Re: methylphosphonate

From: David A. Case (case_at_scripps.edu)
Date: Mon Jul 14 2003 - 19:22:28 CDT

On Mon, Jul 14, 2003, A. Hungie wrote:
>
> 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 

-- 

==================================================================
David A. Case                     |  e-mail:      case_at_scripps.edu
Dept. of Molecular Biology, TPC15 |  fax:          +1-858-784-8896
The Scripps Research Institute    |  phone:        +1-858-784-9768
10550 N. Torrey Pines Rd.         |  home page:                   
La Jolla CA 92037  USA            |    http://www.scripps.edu/case
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