[AMBER] 【tleap】 How to add water(TIP3P) to the right place in the protein?

From: Huimin Tian <201921150072.mail.bnu.edu.cn>
Date: Mon, 29 Nov 2021 10:29:57 +0800 (GMT+08:00)

Dear all,
I have encountered a problem in the tleap program.
I delete the water in pdb first, and then add water with tleap (TIP3P),
the water molecules in many positions inside the protein will not be added,
which will make certain charged residues closer to the active center overcrowded and deviate from their original positions .
After 5ns kinetic simulation, the structure did change.
These charged residues deviate from their original positions,
 which may complicate the study of their chemistry. Is this normal? If it is not normal, what should be done?
Should I choose to retain water molecules near charged residues? How to choose which water molecules to retain? Are there general guidelines?
 Or is there a way to make tleap add water directly to these positions to be consistent with the water in the crystal structure?

Thanks and Regards,

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Received on Sun Nov 28 2021 - 19:00:03 PST
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