Re: [AMBER] Solvate and manipulate order of atoms in Leap

From: David A Case <>
Date: Tue, 3 Aug 2021 08:20:32 -0400

On Sun, Jul 25, 2021, He, Amy wrote:
>I’m using Amber/20 and I’m doing system preparation with the leap
>program. I want to solvate the system, add ions, and I have to change the
>order of a few atoms in the structure, and generate new inputs with the
>re-ordered system.

Sorry to be slow in replying, and I'm unsure whether this question has
already been answered or not.

>However, I didn’t find the BOX information in my parm7 (prmtop) file. And I
>think it’s because I didn’t set the box in the second leap step, by either
>“setbox” or “solvatebox”…

You can use the setbox command in tleap to create a box (even though at this
point it won't have the correct dimensions.) Then use the ChBox command
to get the correct values into the rst7 file. Use the data in the last line
of your first rst7 file to get the data to feed to ChBox.

...good luck...dac

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Received on Tue Aug 03 2021 - 05:30:03 PDT
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