AMBER Archive (2006)

Subject: AMBER: Which one is the best force field for DNA?

From: Chengwen Chen (chenchengwen_at_gmail.com)
Date: Wed Apr 12 2006 - 22:11:14 CDT

 Dear all,

I am modeling the 12-bps B-DNA with platinum bound to it. I wonder is parm98
the best force field for carrying out MD simulation with SANDER in AMBER 8?
Or parm99 is better?
I learned form AMBER 8 manual that ff98 is for nucleic acid and ff99 "points
toward a common force field for proteins for 'general' organic and
bioorganic systems". So ff98 is better ? But the AMBER Tutorial of modeling
DNA use the ff99. So I am confused.

Thank you for your kindly reply.

Best Wishes,
Wendy

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