Rmsd is, as the name tellls, the root of mean square deviation of a given structure or an ensemble of structures from a reference structure. The mean is the average based on a selected set of atoms, often c-alpha or backbones if it is a protein.

But, before you calculate rmsd, you have to align the ensemble with the reference structure, usually using least square method, based on a set of selected atoms.

These calculations can be performed very easily using vmd program, since it has a gui. You just need to have your structures as a pdb and/or dcd trajectory.

g_rms is a free module in gromacs software which compares two structures by computing the root mean square deviation. using of this module is very easy and straightforward.

more information in :

http://www.gromacs.org/Documentation/Gromacs_Utilities/g_rms

sorry , there is a misunderstanding , I need to calculate the RMSD between the crystallized ligand and the docked ligand which docked by Autodock vina and the arranged atoms of the ligand in the hierarchy view of DS was different from that of the reference .

Hi Mohammed,

In this case you have to arrange the atoms of your crystallized structure and docked one. It is not difficult to write a python or any other script to read/write a pdb file.

I agree with Hamed that g_rms is also an easy module to use for calculating rmsd and there is a documentation online.

You may try LigAlign, a tool to compare protein active-sites and investigate ligand binding.

http://www.pymolwiki.org/index.php/LigAlign

http://compbio.cs.toronto.edu/ligalign/

You have a los ot options for caculate RMSD. One is using biopython, other is usign the Gromacs funcionality or the amber_tools funcionality. And the last one is using the VMD trajectory analysis. And sure that you could find a lot of more along the web.

You can use the normal visualising tool PyMol to get the RMSD between your ligands

You can also use MVD software

Try to use PyMol which can be of best choice for calculating rmsd. Use the option align to get the rmsd between two structures.

If you have used AutoDock for docking, then RMSD values are provided in docking log file (dlg) itself. DLG files are standard output files generated for docking runs. Just open the dlg file in any text editor like MS WordPad (Provided inbuild with windows OS). There is separate table named "RMSD Table" in dlg file. Please see the attached figure of dlg file opened in wordpad highlighting RMSD values in red box. "Reference RMSD" column is what you will be interested in...

There is no need to use another separate program to calculate RMSD, in case if you use AutoDock 4.2.

Hi Mohamed,

I want to ask, does your crystallized ligand and docked ligand has the same 2D-structure?

Yes, they are.

Hi,

In Discovery Studio 3.1 -

go to structure > RMSD > biopolymer structure > in the top drop down select reference > in the blow box choose query (structure to be compared - can be one or multiple) > with all residues selected go with C-Alpha/Main Chain

Since the residues are in order and not their individual atoms - DS or you shouldnt have a problem getting these RMSD values. It is only for all-atom RMSD that a 1 to 1 correspondance is required.

Try it and let me know.

Hope this helps.

Best,

/A

In DS vizualizer it is reliable to find RMSD by using superimposition module....

Hi,

You can do it on your own by using the formula attached.

Best Wishes

Just wanted to point out that I believe g_rms from Gromacs does not correct for molecule symmetry.

Dear all,

Concerning this topic, can you explain how to measure RMSD of the best structures from docking using VMD?

Thank you!

Rita.

Hi there, 

There are two ways of using VMD to calculate RMSD. Manual and through scripting. 

Before you can calculate RMSD in VMD:

Load your structures in one go. 

Extensions>Analysis>RMSD Trajectory Tool.

In the box that opens (given the selections are correct : This is by default) press Align and then press RMSD. 

This will use the first of the loaded structures as a reference and compute the remaining structures' RMSD from that. 

Should you want to use the scripting method: 

you will have to make use of the measure command. 

it is already best explained here:

http://www.ks.uiuc.edu/Research/vmd/vmd-1.7.1/ug/node185.html

you can find the scripts included in it as well. 

Remember: You have to align (superimpose) the structures otherwise you will have a higher RMSD (which would also have rotational and translational contributions).

This answer assumes that the structures you are comparing are sequentially identical.

Hope this helps,

Best,

/A

Hello friends,

I want to ask a question.

how to caculate RMSD of each residue's backbone around the average structure without docking ? 

thank you!

 Hi Yao, 

Use VMD. 

This answer assumes you want to measure 1 RMSD value for 1 residue. This means that if there are 500 residues in your protein you will have 500 RMSD values. (Have you looked into RMSF??). I will list the way to calculate what you want for 1 residue and you can repeat that in a loop to get RMSD for all the residues.  

The way to do this would be to load your average structure (reference) first and then load your structure which you want to compare to the reference. Once both structures are loaded create two selections using something like :

set ref [atomselect "resid 1 and backbone"]

set tar [atomselect "resid 1 and backbone"]

The above would create 2 selections. The keyword backbone would ensure that just the 4 atoms from the back bone are selected. Resid 1 means that its only for residue 1. The resid needs to same in both selections for the results to make sense. Note: This number has to match a number in your PDB. ref and tar now are your two selections. molid is assigned when you load structures into VMD. This would be different for the two structures you load in and also depends on how you load. 

You would then follow this up with checking if both selections have an equal number of atoms as RMSD can only be computed on a 1 to 1 basis. If the two selections are equal you would first want to remove any rotations and translations for which you would need 

measure fit $ref $tar     

This would give you a matrix "$fit" which you would apply to 1 of your selection to obtain the new coordinates like  

move $fit  .... There are implications to this step. I don't know if its reasonable to perform this per residue??? Maybe you need to apply this once at the start?? I don't know -- it depends on you and what you are studying .. be careful about this step ....

Once one of the selections has been updated you would need to now measure the RMSD. You can do this by 

measure rmsd $ref $tar 

The method that I listed above assumes that you have two structures only. If you have a trajectory from a simulations VMD can help you there as well. But for that you would have to add more line to the set of commands above. Write back if that is the case and someone maybe able to help you out. 

Best,

/A

Desmond and Gromac both are efficient programs for the calculations of RMSD and MM-PBSA analysis

Use https://ligrmsd.appsbio.utalca.cl/

i obtained a RMSD=40.601 A

what conclusion can i have

what does RMSD physicly means

Samir Zergat It does not have a physical interpretation, but a geometrical one. When you calculate the RMSD, you are comparing common graphs. If you get an RMSD around 40 A, you have compared graphs/structures that are too far apart.

Samir Zergat RMSD tells you how well the two molecules overlap. E.g. if you have a crystal structure of a protein, but you are also testing prediction capabilities, so you predict the protein structure and you compare the two - how well do they correspond to each other. 40 is way large number...