[gmx-users] %exist of hydrogen bonds + No -map specified!

[Justin A. Lemkul]

leila karami wrote:
> Dear Justin
> 
> I'm using your script for obtaining %exist of hydrogen bonds.
> 
> When I use  ./hb.pl structure.pdb -map hbmap.xpm -index hbond.ndx, I
> encountered with
> 
> No -map specified!
> 
> 
> I noted to points being at the begining of script:
> 
> #   1. coordinate file (for atom naming) - MUST be a .pdb file with NO
> CHAIN IDENTIFIERS
> #   2. hbmap.xpm
> #   3. hbond.ndx (modified to contain only the atom numbers in the
> [hbonds...] section, nothing else)
> 
> How to fix it?
> 

Your command is wrong.  It should be:

./hb.pl -s structure.pdb -map hbmap.xpm -index hbond.ndx

Note that you omitted the -s flag originally, thus the search for proper 
arguments likely failed.

-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

========================================