[gmx-users] g_hbond (Version 3.3 vs Version 3.14)

Anil Kumar anil at chem.iitb.ac.in
Thu Dec 20 11:45:49 CET 2007

Dear David,

Thanks for your concern.

i am using g_hbond (After vacuum md, just for one step)

Command with options is

g_hbond -f *.pdb -s *.tpr -num *_num.xvg -hx *_hbhelix.xvg

and when i compare the result of v 3.3.1 and v 3.14, i found there is
difference in *_hbhelix.xvg.

Even for standard helix PDB of octa-alanine capped with ACE and NAC,  v
3.3.1 is giving hydrogen bonds under n-n (Value is 3), n-n+1 (Value is 3)
and rest is showing zero value.

While on contrary v 3.1.4 is giving the correct answer with the value of 6
under the n-n+4.

So, am i doing something wrong or is it bug in v 3.3.1!

thanks in advance,
With Regards

ANIL KUMAR(Research Scholar),
Bio-Organic Lab No-336(2nd Floor),
Dept. of Chemistry,I.I.T.Bombay,Powai,
Ph. No.-022-25764780(Lab)
Hostel#1,Room#297,IIT Bombay,Powai,
Mumbai-400076,Ph.No.:-+91-9819638547 (Mobile)
"Education is a progressive discovery of our ignorance"

- Will Durant

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