Re: topology for DNA

From: Chris Harrison (
Date: Fri Jan 28 2011 - 07:59:06 CST

The standard way to build DNA is to use the RNA topologies then apply
the DEO1 patch to pyrimidines and the DEO2 patch to purines. You'll
need to also properly patch your terminals with 5PHO, 3PHO, 5TER, 3TER,
etc ... whichever are most appropriate for your system.


Chris Harrison, Ph.D.
Theoretical and Computational Biophysics Group
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave., Urbana, IL 61801                          Voice: 217-244-1733              Fax:   217-244-6078
Neelanjana Sengupta <> writes:
> Date: Fri, 28 Jan 2011 17:58:03 +0530
> From: Neelanjana Sengupta <>
> To: NAMD <>
> Subject: namd-l: topology for DNA
> Dear all,
> I am attempting to simulate a B-type DNA with the CHARMM force field, using
> NAMD. However, the topology files corresponding to deoxyribose are not
> directly available (only those for ribose/RNA are available), and hence I am
> unable to create suitable psf files.
> Has anybody done this successfully with NAMD/psfgen?
> Thanks and regards,
> Neelanjana Sengupta

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