Hi William,
It may be a good idea to follow the tutorial at:
http://nmr.chem.uu.nl/~tsjerk/MDCourse/
It doesn't take too much time and will give you a fair idea of using
the program, with the options, the file types, etc.
If you look at the top of the output from pdb2gmx you will see the flags
and values you actually passed on the command line reported back to you,
together with any default values that you didn't override. "eiwit.pdb"
is such a value, although I've no idea why a default structure file
should be named that.
And Mark, maybe a Dutch course could be of benefit. Eiwit is the Dutch
word for protein ;)
(O, and you're welcome to apply for a post-doc position to allow you
to learn some more Dutch).
Cheers,
Tsjerk
--
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623
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