Re: [gmx-users] HYDROGEN BOND EXISTENCE MAP

[Neha Gupta]

Thanks.

On Sat, Apr 1, 2017 at 12:59 PM, Sheeja Vasudevan 
wrote:

>
> Hi Neha,
>
> If I understand correctly pdb file is used for extracting information
> about the topology of the molecule..in this case the atom name and type.
> so it does not matter at which time point of time in your simulation your
> pdb file is generated as long as it is whole molecule.
>
> Best
> Sheeja.
>
> > Hi gromacs users,
> >
> > In the perl script to calculate hydrogen bond %, the command is
> >
> > perl plot_hbmap.pl -s structure.pdb -map hbmap.xpm -index hbond.ndx
> >
> >
> > What should the structure.pdb file contain?
> >
> > How to obtain it?
> >
> > At which point of simulations?
> >
> > Thanks,
> > Neha
> > --
> > Gromacs Users mailing list
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>
>
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Re: [gmx-users] HYDROGEN BOND EXISTENCE MAP

[Sheeja Vasudevan]

Hi Neha,

If I understand correctly pdb file is used for extracting information
about the topology of the molecule..in this case the atom name and type.
so it does not matter at which time point of time in your simulation your
pdb file is generated as long as it is whole molecule.

Best
Sheeja.

> Hi gromacs users,
>
> In the perl script to calculate hydrogen bond %, the command is
>
> perl plot_hbmap.pl -s structure.pdb -map hbmap.xpm -index hbond.ndx
>
>
> What should the structure.pdb file contain?
>
> How to obtain it?
>
> At which point of simulations?
>
> Thanks,
> Neha
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
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> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send
> a mail to gmx-users-requ...@gromacs.org.
>


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[gmx-users] HYDROGEN BOND EXISTENCE MAP

[Neha Gupta]

Hi gromacs users,

In the perl script to calculate hydrogen bond %, the command is

perl plot_hbmap.pl -s structure.pdb -map hbmap.xpm -index hbond.ndx


What should the structure.pdb file contain?

How to obtain it?

At which point of simulations?

Thanks,
Neha
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[gmx-users] Hydrogen bond existence map

[Nidhi Katyal]

Hi all

I would like to create hydrogen bond existence map for interaction of each
residue with my ligand. I am aware that -hbm and -hbn option of g_hbond
along with index file would serve the purpose. But the resulting output
file is giving existence map for each atom of the residue. Instead, I want
one map for residue as a whole. Example if any residue of protein is
forming hydrogen bond with my ligand for certain time through bond A but
for the remaining time it forms through bond B, then I want the map to show
presence of hydrogen bond through one single line during the entire course
of simulation. Is it possible with gromacs?

Thanks in advance
Nidhi
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Re: [gmx-users] Hydrogen bond existence map

[Erik Marklund]

Hi Nidhi,

Only with post processing of named files I'm afraid.

Kind regards,
Erik

On 19 Jun 2014, at 10:48, Nidhi Katyal nidhikatyal1...@gmail.com wrote:

 Hi all
 
 I would like to create hydrogen bond existence map for interaction of each
 residue with my ligand. I am aware that -hbm and -hbn option of g_hbond
 along with index file would serve the purpose. But the resulting output
 file is giving existence map for each atom of the residue. Instead, I want
 one map for residue as a whole. Example if any residue of protein is
 forming hydrogen bond with my ligand for certain time through bond A but
 for the remaining time it forms through bond B, then I want the map to show
 presence of hydrogen bond through one single line during the entire course
 of simulation. Is it possible with gromacs?
 
 Thanks in advance
 Nidhi
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