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AutoDock, AutoLigand, MGLTools, Vina, PyRx and more.
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PostPosted: Thu Jul 23, 2009 10:25 pm 
Millimolar User
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Joined: Thu Jul 23, 2009 4:48 pm
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Dear Gurus,

I posted a version of this question over in the autodock vina forum, and for the part of it I was directed here.

In MGLtools and autodock 4 your docking results were viewable in a nice format such that you could view the poses nicely and the cluster analysis and there was a neat function whereby you can use that & command to create a joint pdb file (one that would join the inhibitor pose currently being viewed to the protein w the flexible residues all into one file). This was very convenient for comparing RMSD between different structures and the original structure.

With Vina results, i haven't been able to figure out how to make a single pdb file of the protein and inhibitor, or how to calculate the RMSD between the original x-ray structure and a vina docked structure, or how to compare the RMSD between two different docked structures.

Does anyone have any hints or tricks on how to do this?

I know I am asking a lot, maybe i can try and simplify:

1. How can one (using ADT or PMV) create a single pdb file that includes your protein structure, flexible residues, and one pose from an autodock vina output.
2. Is there an easy way to determine the RMSD between two pdb files (ones that include a protein and an inhibitor)

Any help would be appreciated.


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Translated by MaĆ«l Soucaze © 2009