[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
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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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