I am going to calculate RMSD between native (from PDB) and my docked complexes. I opened complexes in ArgusLab, removed their proteins, deleted all hydrogen (H) to have analogues with the same number of atoms and finally opened these two ligands (native and docked) in Chimera. With following command
rmsd#0: #1:
RMSD was calculated. However I am not sure about its value. When I label atoms of ligands in Chimera (name of atoms in ArgusLab are correct), labeling is not correct and all carbons are labeled "C" instead of "C1", "C2" and so on. In regard to this labeling, calculation of RMSD is correct?
I think you are using the wrong software. Try PyRx for docking and then export the SDF to MAESTRO (they have free licenses for academics). In MASTRO the RMSD calculation is easy as cake.
Hi Samanehan
I have used chimera, but only for visualization. You can use vmd , charmm or write your own code for rmsd calculation.
Thanks guys for your comments.
Dear Matin I have used PyRx for docking and tried to calculate RMSD with other software like Chimera, profit and....I could calculate it manually too. However its value is high, maybe it is because of wrong docking. I downloaded pdb file (1ACJ.pdb) and separated protein and ligand and did blind-docking. Ligand in the complex (using PyRx) has 180 degree rotation in comparison to ligand in native complex ( :( ).
Dear Poonam, I have downloaded VMD but it needs license.
Any comment is really welcomed
Dear Samaneh Fazeli Farsani ,
I believe that PyRx doesn't give the option to write protein-ligand complex rather you can only export ligand docked conformation which you can merge later by other program such as chimera or manual editing.
Further, when you have protein-ligand complex, why you performed bling docking? Based on my own experiences I will say that PyRx is good but not accurate enough to perform blind docking. So either you perform docking at cavity or change the software. You can try iGemDock (http://gemdock.life.nctu.edu.tw/dock/igemdock.php). It will take time but gives you accurate results for blind-docking.
For RMSD calculations of protein, try Superpose server (http://wishart.biology.ualberta.ca/SuperPose/). In Chimera, you can perform RMSD, first prepare your protein by DOCKPREP option and perform docking and then perform RMSD on the obtained complex by Match Maker option.
Thanks
Thanks dear Pankaj and Georgios
Dear Pankaj, yup you are right. PyRx is not good for blind docking and I noticed that for validation of my docking procedure using crystal complex, I do not need to do blind docking. I found interacting residues and did flexible docking. However I still observe a noticeable rotation in my ligand compared with crustal file :(
And for RMSD calculation, I am not going to find RMSD for protein. Ligand is important for me. Match Maker option works for protein.
VDM is free for academic use.
Please load both PDB files, crystal and docked one (you could use Vina for docking), on VMD. Then, using "RMSD calculator" you can easily find RMSD between both structures.
Hi, Samaneh
In your case, VMD (orPyMol) may be a better tools for RMSD calculation.
http://www.ks.uiuc.edu/Research/vmd/plugins/rmsd/
http://www.ks.uiuc.edu/Training/Tutorials/vmd/tutorial-html/node7.html
Thanks dear Dariush and Ya-Zhou for your useful comments. I am using VMD for RMSD calculation :)
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