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

David van der Spoel spoel at xray.bmc.uu.se
Tue May 6 15:03:30 CEST 2008


sharada wrote:
> 
> 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
I don't know where 120 comes from, it is 180-60. 60 is from Kabsch & Sander.
Anyway definitions differ between programs and the current definition is 
in line with a few recent papers. You can change it however.

> 
> 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 <mailto: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.
>     Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755.
>     spoel at xray.bmc.uu.se <mailto:spoel at xray.bmc.uu.se> spoel at gromacs.org
>     <mailto:spoel at gromacs.org> http://folding.bmc.uu.se
>      
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> 
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> ANIL KUMAR(Research Scholar),
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-- 
David van der Spoel, Ph.D.
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se



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