AMBER Archive (2009)

Subject: Re: [AMBER] (no subject)

From: Thomas Cheatham III (tec3_at_utah.edu)
Date: Wed Feb 25 2009 - 18:48:56 CST

> I am modeling a single-stranded DNA conjugated to an oligopeptide moiety
> via phosphamide bond. I'll use sander for NMR -restrained molecular
> dynamics. Which force field do you recommend me to use.   Thank you

What I would do is use ff99SB with the parmbsc0 nucleic acid force field
modifications. For the connecting residue, you will likely have to
generate new parameters, and I would first try out GAFF/Antechamber with
RESP charges. For more insight into creating parameters, see:

  http://ambermd.org/tutorials/advanced/tutorial1/

--tec3


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