[gmx-users] Example file for DNA

Justin A. Lemkul jalemkul at vt.edu
Sat Oct 17 03:08:05 CEST 2009

David Crosby wrote:
> Hello fellow GROMACS users!
> I've been having a heck of a time with the reformatting of a DNA molecule
> into a GROMACS-compatible format.  I know that residues (bases) must be
> renamed to DTHR, etc., though it would be endlessly helpful if someone could
> please send me an example pdb or gmx file I can use as reference.  Better
> yet, if anyone has a nifty program that will reformat a nucleic acid model
> into the GROMACS format, that would answer my prayers!  The duplex I'm
> working with is only 21nt, so it's not insane to have to modify the file by
> hand...

A simple Perl script can make substitutions, or you can use a text editor like 
vi or a command like sed.  In about 4 commands, the whole file can be re-named. 
  In vi, for example:

:1,$s/DT  /DTHY/g

...and all of your thymines are re-named (note the spacing is important).


> Thanks in advance!
> Dave Crosby
> University of California, Irvine
> Dept of Pathology and Laboratory Medicine
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


More information about the gromacs.org_gmx-users mailing list