Re: [AMBER] How to superpose the solvated box to the original pdb structure?

From: David A Case <>
Date: Tue, 12 Oct 2021 16:31:38 -0400

On Tue, Oct 05, 2021, Gao Zhenting wrote:
>I tested "set default nocenter on" in tleap, but the output solvated
>protein coordinates are still different from the original one.
>Could you help to check?

Looks like I was wrong: the solvateBox command seems to move the solute,
even when "set default nocenter on" is present.

But it's just a rigid translation, so you should be able to use cpptraj to
superimpose the solute on the original structure, then use autoimage to
re-pack the waters around the solute, which is now in back in its original

...good luck...dac

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Received on Tue Oct 12 2021 - 14:00:02 PDT
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