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