I was advised to use a program that would be easier to do molecular docking. I used AutodockTools, but when editing missing atoms in a protein it gives a bunch of errors and stops working, I decided to switch to PyRx and encountered a problem when choosing autogrid and autodock executable files. Gives out a bunch of lines with errors instead of the required window. If anyone has encountered such a problem, can anyone help solve it?
Hi, it is an encoding error, and you can follow the instructions here to solve this issue.
https://stackoverflow.com/questions/21129020/how-to-fix-unicodedecodeerror-ascii-codec-cant-decode-byte
First you can fix missing atoms and residues in Chimera from the Dock Prep option then continue in Autodock tools if you wish.
Marwa Abd El Kader Zaater. I don't have one in Chimera like Dock Prep. I looked up how to install, found that it's only via DOCK. Got a license from them, but all files are for Linux (.tar.gz. archives). But looking in other sources, all have everything in Chimera for some reason, what is wrong I can't understand, or the version is wrong or it must be installed somehow, but on their website with Tools I did not find even close similar options
Maksim Romanyuk would you please tell me which version of Chimera have you downloaded? And if possible put the link from which you downloaded Chimera.
Marwa Abd El Kader Zaater The software says version 1.5 (2022-11-24)
Maksim Romanyuk could you please try downloading version 1.16 from here https://www.cgl.ucsf.edu/chimera/download.html
After preparation in Chimera, you can either use Autodock tools or continue in PyRx (you can delete the version you have and reinstall it from here https://pyrx.sourceforge.io/downloads if you wish) and I hope everything will work smoothly with you.
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