RMSD (Root Mean Square Deviation) Calculation by Discovery Studio Visualizer

How to calculate RMSD value in Angstrom by using Discovery Studio Visualizer after molecular docking of co-crystallized ligand into the active site of target by using MOE (Molecular Operating Environment) or other softwares like Autodock etc. #pharmacy #docking ‪@MajidAli2020‬

[@Dil_k_sur]

I try to do it by discovery studio but the alignment or series of atom was changed. How to correect the series of atom alignment

[@Dil_k_sur]

@bajranglohan333
1 month ago
hello Sir, I am calculating RMSD, but I facing some problem that showing an error...The order of the atoms has to be the same. Use the
Hierarchy View and expand both the reference ligand and
the pose to verify that the atoms are listed in the same order.
Plz, explain it.
Same issue, how to cope up with this

[@arshiaamjad9220]

you should’ve performed docking again with the same ligand using discovery studio, instead of doing it before and just opening the window of done

[@MajidAli2020]

Just open that docking file which is already done

[@BajrangLal-w1s]

@Dr. Majid Ali I am getting problem to calculate RMSD. kindly help me to solve this problem.
Heavy Atom RMSD to All
Name Reference RMSD (A)
1KZN 1 1KZN 1 0.0000
output_a_3_model_0 2 output_a_3_model_0 2 0.0000
The following molecule(s) failed due to element types
not matching the reference ligand.
output_a_3_model_0 2
The order of the atoms has to be the same. Use the
Hierarchy View and expand both the reference ligand and
the pose to verify that the atoms are listed in the same order.

[@BabyDoll-rp4jr]

But sir rmdf and arsd Moe Wala batayn na 2019 version Moe.. plz sir..

[@JYOtiRaNJanMANgaRaj]

Thank you 😊

[@MuhaMedZaKi]

Salam Alaikum, I am looking for a reference to read more about all the parameters that we need to analyze while docking ligand protein

[@sumbalasif5561]

kindly upload a video on gold docking result analysis using discovery studio visualizer if the results are in the form of a single sdf file containing all ligands

[@MajidAli2020]

Ok I will try

[@husseinkyhoiesh]

need program MOE (Molecular Operating Environment) 2019

[@magicdiamond8767]

Hello every one
moe docking give multiple pictures for the same amino acid with same number of residue in peptide when checked ligand interactions, Is that normal or error occure ,cause??

[@learnwithtricksandfun4876]

👍

[@keyadutta3767]

assalamulaikum sir.. sir how can i change protein conformation in discovery studio? also can i use pyrax for docking?

[@keyadutta3767]

sir it is very helpful for me..but i have a little bit confusion about compound..can i use same compound for docking?

[@BabyDoll-rp4jr]

Thank you sir

[@tajmalookkhan8263]

Very helpful 😊

[@kilwa6960]

Dr , how i can communicate with you?

[@amourdouaa4327]

I need a method to calculate Rmsd can you help me please

[@devendraviashnav]

I did docking and found the RMSD values. Is it different from what you explained here or both are same? Please explain in detail.

[@amourdouaa4327]

I need a method to calculate Rmsd can you help me please

[@sumbalasif5561]

very helpful video

[@MajidAli2020]

Thanks

[@amourdouaa4327]

I need a method to calculate Rmsd can you help me please

[@samaadam6947]

I'm sorry but i tried but couldn't don't that can you provide us with written steps or official tutorial

[@MajidAli2020]

You must have problem with your structure

[@samaadam6947]

How i fix that i already downloaded the protein from RCSB PDB​@@MajidAli2020

[@MajidAli2020]

Its not in protein but in your structure

[@samaadam6947]

@@MajidAli2020 how I can solve that

[@MajidAli2020]

It depends on what kind of issue it is

[@bajranglohan333]

hello Sir, I am calculating RMSD, but I facing some problem that showing an error...The order of the atoms has to be the same. Use the
Hierarchy View and expand both the reference ligand and
the pose to verify that the atoms are listed in the same order.
Plz, explain it.

[@alien2883]

Have you fixed it?

[@bajranglohan333]

not yet
@@alien2883