The ligand is interacting with chain A of the protein and the RMSD plot shows a sudden rise in first 20 ns and then stabilizes in the later part. Please tell if chains can be separately viewed in trajectory files?
Dear Ajit Kumar Singh ,
First of all, analyze if you indeed fit the trajectory, afterward extract some frames and realize the visual inspection to confirm if the rise during the simulation is related to using the three proteins.
To separate your proteins, you will use the make_ndx module.
In this step, you will split the protein (splitch 1), and three new options regarding the protein chains will appear. Next, you should analyze if the number of protein atoms matches what you expect.
If not, you will have to separate the protein chains by the residue index (ri).
After that, use the index file during the RMS calculation and select the proper protein chain.
Greetings
Everything can be viewed and analysed separately in gromacs by making index group of your interested entity. Use gmx make_ndx.
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