Hi,
Thank you all for the response, Yes, the backbone of my protien does not have
the required -Hydrogens for the program to calculate the hydrogen bonds. The
option 6 (Mainchain +H) worked for me. Still I am not clear as to what exactly
are cut off angle 30 degrees and cut-off radius .35 nm mean in the program
g_hbond. Is it considering the hydrogen bond angle of 120 +/- 30 ? In that case
cut-off angle 60 & 120 in other versions does not make sense ... Kindly clarify
my doubts
regards
sharada
-- Original Message --
From: "Anil Kumar" <[EMAIL PROTECTED]>
To: "Discussion list for GROMACS users" <[email protected]>
Date: Mon, 5 May 2008 23:13:25 +0530
Subject: Re: [gmx-users] Angle definition in g_hbond ...
Hi,
Just calculate the no. of atoms according to the choice of options and
manually. you will understand why is it giving the error. Secondly check how
gromacs calculate the no. of hydrogen bonds. It uses the cut-off 0.35 nm and 30
in version 3.3.1, but in earlier version the angle cut-off was 60 in version
3.2 and 120 in version 3.1.
regards
anil
IITB, India
On Mon, May 5, 2008 at 7:20 PM, David van der Spoel <<[EMAIL PROTECTED]>[EMAIL
PROTECTED]> wrote:
Mark Abraham wrote:
sharada wrote:
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
I haven't used this tool, but the problem looks like it is here. Are there any
hydrogens in this group?
use 6
Mark
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