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

sharada sharada at ccmb.res.in
Wed May 7 07:49:44 CEST 2008



    
        
            
Hello Dr. David,
Now it is clear to me about the 30 cutoff angle. In some papers the Donor-Hydrogen-Acceptor angle is mentioned as 120 &  anything above it till the linear angle (180). In the latest paper of Prof Gunsteren in Eur Biophys J on Melittin .... there he has considered the angle to be greater than or equal to 135 and the HB distance as smaller than .25nm. Yes the program has the provision to vary these values. Thank you for the clarifications.
have a good day.
sharada
-- Original Message --
From: David van der Spoel <spoel at xray.bmc.uu.se>
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Date: Tue, 06 May 2008 15:03:30 +0200
Subject: Re: [gmx-users] Angle definition in g_hbond ...
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
>         _______________________________________________
>         gmx-users mailing list gmx-users at gromacs.org
>         <mailto:gmx-users at gromacs.org>
>         http://www.gromacs.org/mailman/listinfo/gmx-users
>         Please search the archive at http://www.gromacs.org/search
>         before posting!
>         Please don't post (un)subscribe requests to the list. Use the
>         www interface or send it to gmx-users-request at gromacs.org
>         <mailto:gmx-users-request at gromacs.org>.
>         Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> 
> 
> 
>     -- 
>     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
>      
> 
>     _______________________________________________
>     gmx-users mailing list gmx-users at gromacs.org
>     <mailto:gmx-users at gromacs.org>
>     http://www.gromacs.org/mailman/listinfo/gmx-users
>     Please search the archive at http://www.gromacs.org/search before
>     posting!
>     Please don't post (un)subscribe requests to the list. Use the www
>     interface or send it to gmx-users-request at gromacs.org
>     <mailto:gmx-users-request at gromacs.org>.
>     Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> 
> 
> 
> 
> -- 
> (`.) Always
> `.(`.) Keep
> (`.). Smiling!
> `..
> `.(*.(`. .).*).`
> *.. * ANIL *..*`
> `.(.(.* *.)`.).`
> 
> ANIL KUMAR(Research Scholar),
> Bio-Organic Lab No-336(2nd Floor),
> Dept. of Chemistry,I.I.T.Bombay,Powai,
> Mumbai-400076,
> Ph. No.-022-25764780(Lab)
> Mobile:-09819638547
> -----------------------------------------
> Residence:-
> Hostel#1,Room#297,IIT Bombay,Powai,
> Mumbai-400076,Ph.No.:-022-25721017(Hostel)
> ---------------------------------------------------------------------------
> "Time is money and duty is God.....To rise in life , you must respect 
> both !!!!!"
> ---------------------------------------------------------------------------- 
> _______________________________________________
> gmx-users mailing list gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> 
> 
> ------------------------------------------------------------------------
> 
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
-- 
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
_______________________________________________
gmx-users mailing list    gmx-users at gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-request at gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php

        
    

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20080507/ec82aaed/attachment.html>


More information about the gromacs.org_gmx-users mailing list