Dear Amber community,
I am writing this email to discuss the issue of determining the states of HIS residues in simulations. Recently, I have been using several tools such as H++, PDB2PQR, and Schrodinger to predict the states of HIS residues in the same protein. However, the results provided by these tools are often inconsistent, which has left me confused. I would greatly appreciate your advice and input in determining which tool to use or how to establish the correct state.
While using tools like H++, PDB2PQR, and Schrodinger for prediction, I have encountered the following challenges:
Inconsistent results: The predicted HIS states differ among the different tools. For example, some tools predict the protonated form, while others suggest the deprotonated form. This discrepancy has made it difficult for me to choose the correct state.
Credibility concerns: Each tool has its own algorithm and assumptions, making it challenging to determine which prediction is the most reliable and accurate. I need further guidance to determine which result to trust.
Thank you very much for your assistance!
Warm regards,
Xiaochun Zhang
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Received on Mon Jun 12 2023 - 01:30:02 PDT
