Re: topology for DNA

From: Eduardo Cruz-Chu (chucruz_at_ks.uiuc.edu)
Date: Fri Jan 28 2011 - 08:23:33 CST

There was a link that explained those steps at:

http://www.ks.uiuc.edu/~villa/dna/

the link is a bit outdated, and the tarball with the examples is missing.
However,the way to apply the aliases is still described in the website.

regards;

Eduardo

On Fri, 28 Jan 2011, Chris Harrison wrote:

> 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.
>
>
> Best,
> Chris
>
>
> --
> 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
>
> char_at_ks.uiuc.edu Voice: 217-244-1733
> http://www.ks.uiuc.edu/~char Fax: 217-244-6078
>
>
> Neelanjana Sengupta <senguptan_at_gmail.com> writes:
>> Date: Fri, 28 Jan 2011 17:58:03 +0530
>> From: Neelanjana Sengupta <senguptan_at_gmail.com>
>> To: NAMD <namd-l_at_ks.uiuc.edu>
>> 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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