From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Fri Feb 02 2007 - 09:08:06 CST
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
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
This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:44:21 CST