dear gmx-users,
I have a very fundamental query. I am trying to obtain the backbone hydrogen
bonds formed during a 15ns simulation of a 35 long protein. When I do this by
using g_hbond and selecting the Backbone groups, I am getting no hydrogen bonds
at all . However, when I plot the hydrogen bonds for some of the structures
picked up through the dynamics using InsightII I am able to see the backbone
HBs in almost all of them.
This is the command I am using:
g_hbond -f HBD1_15npep.trr -s HBD1_5mr_md.tpr -n HBD1_10n_nsl.ndx -num
hnum.xvg -g hb.log
this is the output I obtain and the hb.log file is not created :
Reading file HBD1_5mr_md.tpr, VERSION 3.3 (single precision)
Specify 2 groups to analyze:
Group 0 ( Protein) has 358 elements
Group 1 ( Protein-H) has 271 elements
Group 2 ( C-alpha) has 36 elements
Group 3 ( Backbone) has 108 elements
Group 4 ( MainChain) has 144 elements
Group 5 (MainChain+Cb) has 177 elements
Group 6 ( MainChain+H) has 181 elements
Group 7 ( SideChain) has 177 elements
Group 8 ( SideChain-H) has 126 elements
Group 9 ( Prot-Masses) has 358 elements
Select a group: 3
Selected 4: 'Backbone'
Select a group: 3
Selected 4: 'Backbone'
Calculating hydrogen bonds in Backbone (108 atoms)
Found 0 donors and 72 acceptors
No Donors found
-------------------------------------------------------
Program g_hbond, VERSION 3.3
Source code file: gmx_hbond.c, line: 1827
Fatal error:
Nothing to be done
-------------------------------------------------------
"Keep Your Shoes and Socks On, People" (F. Zappa)
Could anyone please let me know the distance and angle definition used in the
program g_hbond. There is a mention about cutoff angle and Cutoff radius as
shown below.
-a real 30 Cutoff angle (degrees, Donor - Hydrogen -
Acceptor)
-r real 0.35 Cutoff radius (nm, X - Acceptor, see next option)
What exactly is the Cutoff angle ? Usually the angle of Donor - Hydrogen
-Acceptor is around 120 degrees and the distance is around 0.2nm. I have
searched the gromacs forum but could not get any help. thanks for your
patience reading.
sharada_______________________________________________
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