Dear Research colleagues,
I have been trying to study the interactions of a ligand with the DNA with PDB id 1BNA using autodock 4.2. I am using mgl tool 1.5.7rc1 and python 2.7.9. I am a novice to these studies and have been following the tutorials available in http://autodock.scripps.edu and youtube. In the process, I faced many error messages whose meaning I could hardly understand. For example, "IndexError: list index out of range", "TypeError: must be string without null bytes or None, not str".
Could anybody help how to understand these error messages and troubleshoot accordingly, or suggest any reference literature for the same.
To my knowledge there is one error references here: http://autodock.scripps.edu/faqs-help/error/
but I am not sure how complete it is. Anyway, I think I recognise one of your error, here is the solution: you should always write your scripts and not copy and paste. Type error is typical of a copy and pasted command.
Make sure the input files are in the correct format. Make sure the path to the files is correct and free of empty spaces. Follow the tutorials step by step. What is your operating system? In which part of the docking procedure do you get the errors? What are the inputs and commands that lead to the errors?
Check you environmental variable for the python and make sure all the executable and structure placed in a single folder.
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