[gmx-users] %hbond number problem

[Justin A. Lemkul]

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

-- 
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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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