Re: [gmx-users] g_hbond: range checking error

[Shubhangi Gupta]

Hi..

 Thanks for the reply. I was unable to download gromacs-5.1.2; when i
clicked on the link, it showed "the site can't be reached."

However I have been able to figure out the solution. The trajectory file I
was using for analysis of protein-solvent hydrogen bonds did not contain
water coordinates. Now with the trajectory file with both protein and water
coordinates, I have been been to calculate the number of hydrogen bonds
using g_hbond.

Regards,
Shubhangi Gupta
PhD Research Scholar (YUS lab)
Dept of Chemistry
Indian Institute of Technology Bombay
Powai, Mumbai-400076.

Mob: +91 9594229609
e-mail ID: ignahbuhs.gup...@gmail.com
   144033...@iitb.ac.in


On Tue, Apr 26, 2016 at 4:31 PM, Shubhangi Gupta  wrote:

> Hi all,
>
>
>  I want to calculate the number of hydrogen bonds between protein
> and solvent. I am using g_hbond (gromacs 5.0.2) with the two groups -
> protein and SOL. When i run the command, I get a *Range Checking error*
>
> *Variable gx has value -3. It should have been within [0 ..19]*
>
> However when i do the same and choose the two groups as protein and
> protein, the command goes through.
>
> Any help is greatly appreciated.
>
> Thanks
>
>
> Regards,
> Shubhangi Gupta
> PhD Research Scholar (YUS lab)
> Dept of Chemistry
> Indian Institute of Technology Bombay
> Powai, Mumbai-400076.
>
>
> e-mail ID: ignahbuhs.gup...@gmail.com
>144033...@iitb.ac.in
>
>
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Re: [gmx-users] g_hbond: range checking error

[Erik Marklund]

Hi,

Strange. Do you get the same error with 5.1.2? If so, can you please file a 
redmine issue (http://redmine.gromacs.org/) and upload the input files that 
generate this error? Assign the issue to me.

Kind regards
Erik Marklund

On 26 Apr 2016, at 12:01, Shubhangi Gupta 
> wrote:

Hi all,


I want to calculate the number of hydrogen bonds between protein
and solvent. I am using g_hbond (gromacs 5.0.2) with the two groups -
protein and SOL. When i run the command, I get a *Range Checking error*

*Variable gx has value -3. It should have been within [0 ..19]*

However when i do the same and choose the two groups as protein and
protein, the command goes through.

Any help is greatly appreciated.

Thanks


Regards,
Shubhangi Gupta
PhD Research Scholar (YUS lab)
Dept of Chemistry
Indian Institute of Technology Bombay
Powai, Mumbai-400076.


e-mail ID: ignahbuhs.gup...@gmail.com
  144033...@iitb.ac.in
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[gmx-users] g_hbond: range checking error

[Shubhangi Gupta]

Hi all,


 I want to calculate the number of hydrogen bonds between protein
and solvent. I am using g_hbond (gromacs 5.0.2) with the two groups -
protein and SOL. When i run the command, I get a *Range Checking error*

*Variable gx has value -3. It should have been within [0 ..19]*

However when i do the same and choose the two groups as protein and
protein, the command goes through.

Any help is greatly appreciated.

Thanks


Regards,
Shubhangi Gupta
PhD Research Scholar (YUS lab)
Dept of Chemistry
Indian Institute of Technology Bombay
Powai, Mumbai-400076.


e-mail ID: ignahbuhs.gup...@gmail.com
   144033...@iitb.ac.in
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Gromacs Users mailing list

* Please search the archive at 
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