I want to calculate rmsd vale to validate my docking methodology. Number and types of atoms are same but the ID's are different that's by Discovery Studio visualizer not able to calculate rmsd value.
So, do you suggest for that situation how to calculate rmsd vale for small ligand molecules? and nextly, How i use chimera to calculate rmsd for small molecules?
why dont you use pymol? it's quite easy and straightforward
https://www.pymol.org/
RMSD = root-mean-square-deviation. If one knows x, y, z coordinates of the corresponding atoms, one can calculate distances between them [distance = (dx**2 + dy**2 + dz**2)**0.5] . . . and having the distances, one can calculate RMSD . . .
Hi Amit,
You should check the following links for RMSD:
http://chembytes.wdfiles.com/local--files/vmd/vmd-basic_tutorial-1_0.pdf
https://github.com/charnley/rmsd
http://www.math.unm.edu/~vageli/codes/codes.html
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