I have carried out mutation on single amino acid residue in a native protein published in RCSB. Then, for achieving native structure of a mutated structure I carried out MD simulation. Now I have all pdb of the entire span of a few nanosecond MD simulations. I want to check change in position of a single amino acid residue by RMSD change. Please suggest some methods.
In antechamber should be possible or if you want to calculate the RMSD between two structures you can make by an atom-by-atom procedure using the maestro schroedinger graphical intereface, it is free for academics.
Or you can edit the pdb file of the two structures, delete everything but the residue and then use a openbabel
Ciao
Rino
In antechamber should be possible or if you want to calculate the RMSD between two structures you can make by an atom-by-atom procedure using the maestro schroedinger graphical intereface, it is free for academics.
Or you can edit the pdb file of the two structures, delete everything but the residue and then use a openbabel
Ciao
Rino
Every simulation code I know of has the ability to calculate RMSD of whatever atoms you select. Which program are you using?
You can measure what you need using g_rms (to get the time series) or g_rmsf -od (to simply get the average value). Make a custom index group for whatever residue(s) you like. The Gromacs manual explains everything; this sort of analysis is very rudimentary.
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