I have performed docking using autodcok vina resulting in more than 5000 poses. Now I need to calculate the RMSD of the docked poses with one present in crystal structure.
Is there any web server or free software to do that ?
well we do it via VMD or Chimera software by loading the reference and target pdb(s), superimposing the two and then calculating the RMSD value.
i have 500 compounds and will be impossible to do load everything manually and calculate RMSD. i need more faster and simpler method to do the job
Oh, come on, 500 is not that much :]
You can simply concatenate your pdb files into multiframe pdb (even using bash - it shouldn't take more than 3 lines of code and a couple of seconds to do this) - and use it in any software you like.
Hi Nitin, if your problem is solved then may you please share the solution here?
hey Nitin
how did you solve this problem, please share. I have same problem.
Hi Sana and other researchers
read all the comments in the post below and you will find answer to this problem
https://www.researchgate.net/post/SOLVEDWhy_Autodock_gives_Different_RMSD_values_for_same_docking_Which_RMSD_to_take_and_why
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