For VMD,

load the molecule, go to Extension menu, Analysis ----->RMSD calculator and set the number and click RMSD.

For ligand, load and do the same process.

Thank you Chaturvedi for your kind help, would you please give me some detail regarding the setting of number in case of ligand not for protein.

For ligand, you should use Pymol

Load both ligand structures and type on command line

fit ( ligand1), ( ligand2)

It will provide you rmsd.

Dear Chaturvedi,

Thank you for your assistance. I tried it but it shows "ExecutiveRMS-Error: No atoms selected." I don't know what is the problem. I have attached both ligands and will be grateful if you point out my mistake.

Hi

Normally, fit, rms, and rms_cur require that all atom identifiers match.

Because of different identifiers in both ligands, error was showing. For this type of problem you will have to use matchmaker.

rms_cur docked, crystal, matchmaker=4

Hi,

several software can calculate RMSD as you want. But, for a "command line" use... try this python script!

http://baoilleach.blogspot.it/2012/01/whats-up-dock-calculate-rmsd-between.html

http://baoilleach.blogspot.it/2012/01/whats-up-dock-calculate-rmsd-between.htm

try DOCK 6 (for calculating RMSD)

see following link for details (read all comments to know which are relevant to you)

https://www.researchgate.net/post/SOLVEDWhy_Autodock_gives_Different_RMSD_values_for_same_docking_Which_RMSD_to_take_and_why

Dear Chaturvedi, 

Thank you very much for your help. I used rms_cur docked, crystal, matchmaker=4  in the command line and got rms more than 4.

Dear Mattia Sturlese,

Thank you for the link you provided. The blog is indeed very helpful.

You can use TM-Score program inserver

http://zhanglab.ccmb.med.umich.edu/TM-score/

This link you can calculate TM-Score and RMSD. It is the best way to compare two structures: RMSD and TMscore

Dear Roosevelt Alves da Silva,

TM score is TM-score is designed for protein comparison not for ligand.

Thanks Sandeep Singh your link is very helpful.

You are right. I do not pay attention in your question.

In Pymol, to compare two ligands that do not have compatible atom labels, you can use pair_fit to explicitly define which atom of ligand 1 to fit to which atom of ligand 2:

pair_fit (selection), (selection), [ (selection), (selection) [ ...] ]

example:

pair_fit ligA////C1, ligB////C8, ligA////C2, ligB////C4, ligA////C3, ligB////C10

When determining rmsd values, be careful: many alignment algorithms that are mainly used to give you the most meaningful structural alignment for visualisation will refine the alignment by throwing out atom pairs that diverge more than a given cut-off, resulting in unreasonably low rmsds. So when quoting rmsd values, make sure that you indicate exactly how you are aligning!

e.g. in pymol, aligning the same two molecules

super /DDrF0013a//A/13-418/CA, /DDrF0013b//B/13-418/CA

RMS = 0.984 (387 to 387 atoms) out of 409

throws out 22 Calpha positions, thereby "improving" the rmsd from 2.896 to 0.984 compared to an alignment that is forced to retain all atoms.

fit /DDrF0013a//A/13-418/CA, /DDrF0013b//B/13-418/CA, matchmaker = -1, cycles=0, cutoff=100.0

RMS = 2.896 (409 to 409 atoms)

So: Be careful what you are aligning, and make sure your "definition" of rmsd is meaningful.

Dear Annemarie Honegger,

Thank you for your help.

i agree with mr. sandep to try DOCK 6

Discovery Studio has easiest way to calculate RMSD between two ligands or proteins. To calculate RMSD between two small molecules the steps are

Load reference molecule >> structure>> RMSD>> set reference.

Then drag docked molecule to the same window>> select it >> structure>> RMSD>> all atoms or heavy atoms.

The RMSD will be shown to the Right side window.

Hello Fatima,

See this link it will be helpful

http://www.calgorithms.com/blog/2014/06/12/how-to-easily-align-two-molecular-structures-in-vmd/

Dear Mohammad Firoz Khan,

Thank you for your help with Discovery Studio. 

Dear Farah Yousef,

What does it mean you got 8 complexes in the negative side of the binding energy? can you explain?

Use ligrmsd:

Article LigRMSD: A web server for automatic structure matching and R...

Why are RSMD values different when I calculate in different softwares? for example in Discovery Studio and PyMOL

If you get significantly different RMSD values, look at exactly which atoms of one molecule are superimposed on which atoms of the other by the two methods, and which, if any, atoms are excluded from the superposition.

Jean P Ramos-Galarza The differences in RMSD values among the software are mainly due to which atoms are matched for computing the RMSD. You must know which algorithm is used for matching (or at least which pairs of atoms are matched) if you want to explain the values or differences in RMSD. Sometimes, the atoms are not matched correctly by the algorithm used by one software, because the context of interactions even for similar ligands changes from one receptor to others. With the implementation of LigRMSD server ( https://ligrmsd.appsbio.utalca.cl/ ), we are on the way of solving the more critical cases and giving to the users the information needed for evaluating if the match is correct.

For the RMSD calculation you can use the tool ProRMSD in the recent web server we have developed (https://pegasus.lbic.unibo.it/pacdock/index.php).

•https://seq2fun.dcmb.med.umich.edu//DockRMSD/

Use this tool. if the atom pairs doesn't have matching numbers/orders. Add polar Hydrogens for the co-crystal ligand