[gmx-users] readHBmap

mmousivand93 mmousivand93 at ut.ac.ir
Wed Sep 19 02:13:13 CEST 2018

Dear users 

I am going to analysis H-bond and Hbond occupancy using READHBMAP,I
downloaded and extracted READHBMAP.TAR.GZ but after typing:
./readHBmap.py -hbm hbmap.xpm -hbn hbond.ndx -f md6.gro -o occupancy.xvg
-op pairs.dat ,the message "No hydrogen bonds found above the threshold
of 10.0 %%"  will appear. The pairs.dat and occupancy.xvg files are
empty. When I  opened the occupancy.xvg by ConTexT ,the following
results could be seen:" 

Results for readHBmap.py (Author: Ricardo O. S Soares)
--> Found 9 valid hydrogen bond pairs with occupancy of more than 10.0%
--> The hydrogen bond map (hbond.xpm) has 5001 frames 

Pair ID | donor-acceptor | Atom Number | Occupancy (%) | Pair ID 

 I would appreciate any suggestions.  

Best regards

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