Re: [gmx-users] COMMAND IN HBOND

[Neha Gupta]

Thank you for the response.

Can you please send the url link for the location of the script (to
calculate the percentage of hydrogen bond)?

Thanks,
Neha

On Sat, Mar 25, 2017 at 1:36 PM, Tasneem Kausar 
wrote:

> If you want to calculate hydrogen bond invloving residue there are two
> steps
> From gmx hbond you can obtain an xpm file where hydrogen bond existance mad
> is plotted.  Then calculate the percentage of hydrogen bond involving
> residues from script given by justin.
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Re: [gmx-users] COMMAND IN HBOND

[Tasneem Kausar]

If you want to calculate hydrogen bond invloving residue there are two steps
>From gmx hbond you can obtain an xpm file where hydrogen bond existance mad
is plotted.  Then calculate the percentage of hydrogen bond involving
residues from script given by justin.
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Re: [gmx-users] COMMAND IN HBOND

[Neha Gupta]

Hi,


Thank you for the reply.

Actually, we get the number of hydrogen bonds in .xvg file using

gmx hbond -s prd.tpr -f prd.xtc -n index.ndx -num hbnum.xvg
.

Can we generate an output file similar to that, which prints the bonding
residues of protein and ligand?


Thanks,
Neha



On Fri, Mar 24, 2017 at 8:05 PM, Erik Marklund 
wrote:

> Dear Neha,
>
> Gromacs doesn’t offer that much in terms of viewing. This sounds more like
> a PyMol/VMD/Other question.
>
> Kind regards,
> Erik
> __
> Erik Marklund, PhD, Marie Skłodowska Curie INCA Fellow
> Department of Chemistry – BMC, Uppsala University
> +46 (0)18 471 4539
> erik.markl...@kemi.uu.se
>
> On 24 Mar 2017, at 14:33, Neha Gupta > wrote:
>
> Hi gromacs users,
>
> What is the command to view the residues of protein and atoms of ligand
> involved in hydrogen bond?
>
> Thanks,
> Neha
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> send a mail to gmx-users-requ...@gromacs.org gromacs.org>.
>
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Re: [gmx-users] COMMAND IN HBOND

[Erik Marklund]

Dear Neha,

Gromacs doesn’t offer that much in terms of viewing. This sounds more like a 
PyMol/VMD/Other question.

Kind regards,
Erik
__
Erik Marklund, PhD, Marie Skłodowska Curie INCA Fellow
Department of Chemistry – BMC, Uppsala University
+46 (0)18 471 4539
erik.markl...@kemi.uu.se

On 24 Mar 2017, at 14:33, Neha Gupta 
> wrote:

Hi gromacs users,

What is the command to view the residues of protein and atoms of ligand
involved in hydrogen bond?

Thanks,
Neha
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[gmx-users] COMMAND IN HBOND

[Neha Gupta]

Hi gromacs users,

What is the command to view the residues of protein and atoms of ligand
involved in hydrogen bond?

Thanks,
Neha
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