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

leila karami karami.leila1 at gmail.com
Thu Apr 12 13:01:05 CEST 2012

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
#   2. hbmap.xpm
#   3. hbond.ndx (modified to contain only the atom numbers in the
[hbonds...] section, nothing else)

How to fix it?

Best regrads

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