I have a protein and I want to check the orientation of side chain of a particular resdiue A with respect to the residue B in the active site. any help on this regard? currently I am using gmx gangel where group 1 includes the alpha carbon position of B residue and alpha carbon position of A residue and group 2 includes alpha carbon of B and the last atom of the A residue. I am not sure if this is the correct way. any guidance would be appreciated.
Your approach using gmx gangle seems reasonable for analyzing the orientation of side chains between residues A and B in the active site. By defining groups based on alpha carbons and other relevant atoms, you can calculate angles to assess their orientation. Ensure that the chosen atoms represent the orientation you want accurately. Additionally, consider consulting relevant literature or discussing with peers to validate your methodology and interpretation for a more robust analysis.
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