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).
-Justin
Thanks in advance!
Dave Crosby
University of California, Irvine
Dept of Pathology and Laboratory Medicine
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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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