From: Asmi Mahmood (asmi_mahmood_at_yahoo.com)
Date: Mon Nov 02 2020 - 04:41:35 CST


Hope you are doing good. i am having a confusion regarding RMSD calculation in RMSD trajectories tool of vmd.
When i choose my psf+pdb file and open the RMSD trajectories tool  it shows 'protein' by default. my question is that does it mean only protein and not ligand.
Second question is that how can we find rmsd of the whole complex (protein+ligand) excluding water. In that case shall we choose backbone, trace or noh.
my last question that is extension of above questions further divided in two parts that
1) how can we calculate rmsd of ligand alone from a complex (protein + ligand)
2) if i have done simulation of a ligand molecule alone (without protein) then how could we measure its rmsd and what options we shall select in backbone, trace or noh.

Asma Tariq

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