[gmx-users] Angle definition in g_hbond ...

[sharada]

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" <chemanil at gmail.com>
To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
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 <<spoel at xray.bmc.uu.se>spoel at xray.bmc.uu.se> 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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             -- 
 David van der Spoel, Ph.D.
 Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
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