Re: Generation of .psf file of DNA

From: Jian Liu (bay__gulf618_at_sina.com)
Date: Thu Jul 09 2009 - 07:43:21 CDT

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,
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


This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:53:00 CST