Re: Rmsd calculation

From: Asmi Mahmood (asmi_mahmood_at_yahoo.com)
Date: Wed Nov 04 2020 - 04:12:00 CST

Thanks Atanu. I really acknowledge this step by step explanation. Regards

Asma Tariq

    On Wednesday, 4 November 2020, 12:14:53 pm GMT+5, Atanu Maity <atanuchem48_at_gmail.com> wrote:
 
 Hi Asma,
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. 
        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 + ligand) 
          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 backbone, 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 state. 
Regards,Atanu  
On Wed, Nov 4, 2020 at 11:51 AM Asmi Mahmood <asmi_mahmood_at_remove_yahoo.com> wrote:

Hi

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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-- 
Atanu MaityPostdoctoral FellowDepartment of Chemistry, IIT BombayPowai, Mumbai - 4000076  

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