Re: Generation of .psf file of DNA

From: Chris Harrison (charris5_at_gmail.com)
Date: Thu Jul 09 2009 - 09:42:10 CDT

Sudipta,

To elaborate a little further, you first build the RNA structure in your
psfgen input file, then patch each residue of it as indicated by Jian,
converting each RNA residue into a DNA residue.

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
2009/7/9 Jian Liu <bay__gulf618_at_sina.com>
> Hi Sudipta
> Two patches (DEO1 and DEO2) are just to deal with your problem.
> Please refer
>
> http://www.ks.uiuc.edu/Research/namd/2.7b1/ug/node18.html#SECTION00072150000000000000
> and
>
> http://www.ks.uiuc.edu/Training/Tutorials/namd/namd-tutorial-unix-html/node22.html
> to find to way of using "patch".
>
> Enjoy it
> J. Liu
>
>
> ----- Original Message -----
> From: sudipta <sudipta.mml_at_gmail.com>
> To: namd-l_at_ks.uiuc.edu
> Subject: namd-l: Generation of .psf file of DNA
> Date: 2009-7-9 14:53:25
>
> Hi All,
> 燑br>I want to generate psf file for DNA using CHARMM force field. The
> topology file for nuclic acid contains the connectivity of ribose sugar. But
> I need the connectivity of deoxyribose sugar. So I have to replace the OH
> (O2'-H2') group by H (H2') atom.
>
> Can anyone pls suggest me what will be the keyword or command that will be
> written in the *.in *file so that I can get the psf file of DNA.
>
> Thanks,
> Sudipta
>

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