From: Atanu Maity (atanuchem48_at_gmail.com)
Date: Tue Nov 03 2020 - 19:42:33 CST
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
Yes, that means protein only, not ligand. If you want to select
both of them you have to type 'protein or resname "resname of the ligand" '
in the selection box.
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.
The selection will be similar as mentioned above. If you have
multiple ligands, you can avoid typing their resname by simply using
selection 'all and not water' provided you do not have ions and other
cofactors. In case, you have those you have to exclude them also from the
selection and then it is better to mention ligands separately like 'protein
or resname lig1 or resname lig2' etc. In that case, it is better not to
choose anything from the checkboxes rather include them in the selection
(Backbone of protein and ligand excluding hydrogen). The selection may look
like '(protein and name C N CA) or (resname lig and noh)'.
1) how can we calculate rmsd of ligand alone from a complex (protein +
The selection, in this case, will be 'resname lig and noh'. There
is one important thing about alignment before rmsd calculation here. If you
want to really see how the dynamics of the ligand is in the binding pocket
you should not align with respect to ligand. You should align it wrt the
protein+ligand or the protein only.
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
trace or noh.
In this case, simply type 'resname lig' and check the 'noh' box.
Also do not forget to align before calculating rmsd. This way you will be
able to compare the rmsd of the ligand in fee state and in protein-bound
On Wed, Nov 4, 2020 at 11:51 AM Asmi Mahmood <asmi_mahmood_at_remove_yahoo.com>
> 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 +
> 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
> Sent from Yahoo Mail on Android
-- Atanu Maity Postdoctoral Fellow Department of Chemistry, IIT Bombay Powai, Mumbai - 4000076
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