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Problem with flexible docking (Windows 0.93)

PostPosted: Sat Feb 13, 2016 8:16 pm
by david1985
Hello,
I'm using PyRx 0.93 on a Windows notebook. I like the Software very much! When docking ligands at a GPCR with about 300 amino acids in the "normal mode" , i.e. without flexible residues, this works quite well. But then I wanted to perform flexible docking, whrereas I flexed about 10-15 residues. My first problem there was that I got an error and the docking of the same ligand always restarted. I could fix this by changing BEGIN_RES %s %s%4s by BEGIN_RES %s %s %s in the file MoleculePreparation.py. Is this the right solution?
But my biggest problem in flexible docking was, that I entered the Vina search space, but afterwards when looking in the conf.txt file I can see, that the standard values of Center_x_y_z and Dimension_x_y_z are used and the Ligand is docked anywhere in and around the receptor. Is there a solution to this problem?

Thank you very much for help!

Re: Problem with flexible docking (Windows 0.93)

PostPosted: Sun Feb 14, 2016 7:07 pm
by sargis
Hello,

Thank you very much for using PyRx 0.93! I really appreciate your feedback David.

david1985 wrote:When docking ligands at a GPCR with about 300 amino acids in the "normal mode" , i.e. without flexible residues, this works quite well. But then I wanted to perform flexible docking, whrereas I flexed about 10-15 residues. My first problem there was that I got an error and the docking of the same ligand always restarted. I could fix this by changing BEGIN_RES %s %s%4s by BEGIN_RES %s %s %s in the file MoleculePreparation.py. Is this the right solution?

You are correct. I checked the code; if the reside number is more than 3 digits long, %s%4s won't work and your solution is right.
david1985 wrote:But my biggest problem in flexible docking was, that I entered the Vina search space, but afterwards when looking in the conf.txt file I can see, that the standard values of Center_x_y_z and Dimension_x_y_z are used and the Ligand is docked anywhere in and around the receptor. Is there a solution to this problem?

Sorry about this. It's a new bug I made while implementing an option to work with multiple receptors at once. I made a bug-fix for this and created a new update. Please update using PyRx->Help->Check for Updates... option to apply this fix.

Please let me know if you have questions or need more information.

Thank you very much for your feedback!