gromacs564 wrote:
Dear Justin
I download the script "plot_hbmap.pl" and input "perl $0 -s
b4md.pdb -map hbmap.xpm -index hbond.ndx\n",
but the output info is "Unrecognized switch: -bash (-h will show valid
options).";
then,I input "perl\n plot_hbmap.pl -s b4md.pdb -map hbmap.xpm
-index hbond.ndx\n",and the output info is nothing?
So, could you tell me the correct usage? Very thanks!
There are protein and sol in b4md.pdb file.The hbond.ndx file only
contain the [ hbonds_Protein ] section:
1 2 603
1 2 619
1 2 634
1 2 635
1 2 1299
1942 1943 1917
1937 1939 113
1937 1939 114
-------------------------------------
xiaodu
My simulation system contains protein, dna and water.
I used your script already for obtaining %exist hydrogen bonds between
protein and dna
Then doesn't this imply that you know how to run it? Neither of the above
commands is correct. The first uses $0, which is a perl construct for the name
of the program. The second contains a newline (\n) character, although the
format of this command is what you should use (without the newline, which is
printed by the program to the screen as help information).
-Justin
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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