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

2008-05-06 Thread sharada 





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 <[EMAIL PROTECTED]>
To: Discussion list for GROMACS users 
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" <[EMAIL PROTECTED]>
> To: "Discussion list for GROMACS users" 
> 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] > 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.
> [EMAIL PROTECTED]  [EMAIL PROTECTE

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

2008-05-06 Thread 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" <[EMAIL PROTECTED]>
To: "Discussion list for GROMACS users" 
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) has36 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.
 <[EMAIL PROTECTED]>[EMAIL PROTECTED]<[EMAIL PROTECTED]>[EMAIL PROTECTED]   
http://folding.bmc.uu.se



 

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