Dear Ahmad,

the error message means exactly what it says: the model contains perfectly overlapping atoms, many perfectly overlapping atoms. That isn't very realistic and requires your attention! My suggestion is: please have a closer look at the model and resolve the outstanding clashes.

Good luck!
Pavel

On 8/20/19 22:17, Ahmad Khalifa wrote:

Hello,

I attached the log file below. 

Best regards.

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