> 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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Received on Fri Feb 27 2009 - 01:10:38 PST
