Re: DNA hydrogen bonds

From: Peter Freddolino (
Date: Fri Feb 02 2007 - 09:08:06 CST

Hi Maxim,
I may not understand your question properly... if you build DNA using
the standard charmm topology files, it will represent hydrogen bonding
interactions in double stranded DNA through a combination of VDW and
electrostatic interactions. There's no patch needed to get hydrogen
bonding, and indeed, the modern CHARMM forcefield *has* no term for
hydrogen bonding.

Maxim Karachevtsev wrote:
> Hi all!
> Could sombedy let me know if in NAMD (topology file) is a patch which can help to model two different strands of DNA (hydrogen bonds between nucleic bases of different DNA strands).
> If there is not such patch how to write it by myself (main principles)
> Thank you
> Maxim

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