Decomposition

[Naresh K N]

I have successfully completed per residue decomposition analysis. How do I get the pdb file of the complex with bfactor and energy contribution from each residue towards the binding energy with ligand. I need a 3D image of protein with ligand bound in the pocket with interacting residues highlighted with colour gradation indicating energy contribution.

Thanks a lot in advance.

And thanks a lot for such a wonderful software to carry out MMPB(GB)SA.

[Mario Ernesto]

You can use gmx_MMPBSA_ana (https://valdes-tresanco-ms.github.io/gmx_MMPBSA/dev/analyzer/#gmx_mmpbsa_ana-the-analyzer-tool) to analyze the results and extract the pdb with the per-residue decomposition energy

https://www.youtube.com/watch?v=Ww7juWeWQQ8&ab_channel=BioinformaticBrothers

--
You received this message because you are subscribed to the Google Groups "gmx_MMPBSA" group.
To unsubscribe from this group and stop receiving emails from it, send an email to gmx_mmpbsa+...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/gmx_mmpbsa/3aa9ca63-e582-4173-80f7-a6948a009178n%40googlegroups.com.
For more options, visit https://groups.google.com/d/optout.

[Naresh K N]

The pdb file of the complex that we get, is it the structure as obtained at the end of MD trajectory or is it an average structure?

[Mario Ernesto]

It is the first frame

To view this discussion on the web visit https://groups.google.com/d/msgid/gmx_mmpbsa/3b7eff53-d787-4e30-947b-31295bc61b7an%40googlegroups.com.

[Naresh K N]

In which case the PyMol image of the complex does not reflect the energy plot right ?

[Mario Ernesto]

I'll assume it does reflect the energy correctly, but you can always use the pdb to generate the image according to your needs

To view this discussion on the web visit https://groups.google.com/d/msgid/gmx_mmpbsa/638c0d6e-f2e7-43f4-8d28-032a4adeb359n%40googlegroups.com.