How to analyse a molecular dynamics of docked proteins?

More Andre Azevedo Reis Teixeira's questions See All

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How to analyze a particular region of my simulation box in GROMACS?

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Why might my GFP tag be dissociating from my plasmid after transfection?

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Precipitate after adding laemmli buffer to protein solution containing Potassium Acetate?

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What is the most suitable server for predicting protein structures in bacteria?

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Do you need the CMV enhancer before the CMV promotor for a proper function of CMV on the gene that follows?

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How does GROMACS calculate the average structure of proteins?

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How to replicate the well conditions of a crystal hit with 20%(w/v) isopropanol?

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25 February 2021 9,761 1 View

Bharath B.R

Plot PMSD and RMSF plots before and after docking and compare

Rodrigo Faccioli

You can check atom interactions between your molecule and protein.

If your set of molecules is lower you can check using Pymol, for example.

Andre Azevedo Reis Teixeira

How long would guys think its enough? 30 ns is too short?

Better

I agree with Bharath in terms of ns. I suggest you create RMSD plot to see the stability of System.