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

From: Carlos Simmerling <>
Date: Mon, 29 Nov 2021 05:38:35 -0500

You can retain all of the crystal water if desired.

On Sun, Nov 28, 2021, 9:30 PM Huimin Tian <>

> 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,
> Tian
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Received on Mon Nov 29 2021 - 03:00:02 PST
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