[gmx-users] Example file for DNA

David Crosby dcrosby at uci.edu
Sat Oct 17 02:45:12 CEST 2009

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

Thanks in advance!
Dave Crosby

University of California, Irvine
Dept of Pathology and Laboratory Medicine

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