AMBER Archive (2003)

Subject: methylphosphonate

From: A. Hungie (hungie01_at_hotmail.com)
Date: Mon Jul 14 2003 - 08:20:52 CDT

Dear All,

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?
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?
Thank you very much in advance for your kindness.

Sincerely Yours,
Hungie

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