Contact map of two peptides interacting in a dimer

[Roshan Shrestha]

Dear all,
            I have a trajectory for the simulation of a membrane protein dimer inside a bilayer. I am trying to plot contact map between two interacting peptides in the dimer.  For now, I am trying to implement the method given in https://www.mdanalysis.org/mdanalysis/documentation_pages/analysis/contacts.html 
            I know that the contact map that I will generate will have a cut-off. This is a value similar to the Gromacs MD cut-off value for non-bonded interactions. But, I don't know how to define two peptides for contacts in the program. In VMD, I simply used VMD plugin where I used trjconv to get trajectory of two peptides and load them into it to plot contact maps.
           Any suggestions will be extremely helpful. Thanks

[Max Linke]

Our contact analysis only counts the number of contacts. It doesn't produce a contact-map like you see in VMD.  You can use instead the distance functions to calculate a distance matrix (VMD calls those contact maps)

https://www.mdanalysis.org/mdanalysis/documentation_pages/analysis/distances.html

```python

from MDAnalysis.analysis import distances

pep1 = u.select_atoms('do your selection of peptite 1')

pep2 = u.select_atoms('replace the selections!')

cmap  = distances.distance_array(pep1, pep2, box=pep1.dimensions)

fig, ax = plt.subplots()

ms = ax.matshow(cmap)

plt.colorbar(ms)

# if you are not in an jupyter notebook

plt.show()

```

cmap will contain the distances between each atom defined in `pep1` and `pep2`. There hasn't been any cutoff applied yet. You have to decide yourself what to do with the distance matrix! For example to only show the formed contacts you can use:

```python

cutoff = 1  # ANGSTROM

contacts = cmap < cutoff

fig, ax = plt.subplots()

ms = ax.matshow(contacts)

plt.colorbar(ms)

# if you are not in an jupyter notebook

plt.show()

```

best Max

--
You received this message because you are subscribed to the Google Groups "MDnalysis discussion" group.
To unsubscribe from this group and stop receiving emails from it, send an email to mdnalysis-discus...@googlegroups.com.
To post to this group, send email to mdnalysis-...@googlegroups.com.
Visit this group at https://groups.google.com/group/mdnalysis-discussion.
For more options, visit https://groups.google.com/d/optout.

[Roshan Shrestha]

Thank you Max. I am little bit struggling with making selection of two peptides. In Gromacs, what I usually used to do is make index file of two peptides like a 1-449 for one peptide and a 450-898. for another. Can you suggest me how to make such selection between these two peptides in mdanalysis?
Thanks

[Max Linke]

We have a comprehensive selection language for this. Have a look in the docs. That should help.

https://www.mdanalysis.org/docs/documentation_pages/selections.html#selection-commands-label

--

[Roshan Shrestha]

Thank you Max. Cheers !!!

On Tuesday, January 2, 2018 at 11:11:40 PM UTC+5:45, Max Linke wrote:

We have a comprehensive selection language for this. Have a look in the docs. That should help.

https://www.mdanalysis.org/docs/documentation_pages/selections.html#selection-commands-label

On Tue, Jan 2, 2018 at 9:55 AM Roshan Shrestha <rosh...@gmail.com> wrote:

Thank you Max. I am little bit struggling with making selection of two peptides. In Gromacs, what I usually used to do is make index file of two peptides like a 1-449 for one peptide and a 450-898. for another. Can you suggest me how to make such selection between these two peptides in mdanalysis?
Thanks

On Monday, January 1, 2018 at 10:20:47 AM UTC+5:45, Roshan Shrestha wrote:

Dear all,
            I have a trajectory for the simulation of a membrane protein dimer inside a bilayer. I am trying to plot contact map between two interacting peptides in the dimer.  For now, I am trying to implement the method given in https://www.mdanalysis.org/mdanalysis/documentation_pages/analysis/contacts.html 
            I know that the contact map that I will generate will have a cut-off. This is a value similar to the Gromacs MD cut-off value for non-bonded interactions. But, I don't know how to define two peptides for contacts in the program. In VMD, I simply used VMD plugin where I used trjconv to get trajectory of two peptides and load them into it to plot contact maps.
           Any suggestions will be extremely helpful. Thanks

--
You received this message because you are subscribed to the Google Groups "MDnalysis discussion" group.

To unsubscribe from this group and stop receiving emails from it, send an email to mdnalysis-discussion+unsub...@googlegroups.com.