[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.gupta6 at gmail.com
               144033008 at iitb.ac.in


On Tue, Apr 26, 2016 at 4:31 PM, Shubhangi Gupta <ignahbuhs.gupta6 at gmail.com
> 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.gupta6 at gmail.com
>                144033008 at iitb.ac.in
>
>