Re: [AMBER] How to specify the protein position in box while using tleap

From: David A Case <>
Date: Tue, 3 Jul 2018 08:49:35 -0400

On Tue, Jul 03, 2018, Jinfeng Chen wrote:
> I want to create a cubic box, and make the protein somewhere other than the
> center of the box ,

Be aware that, physically, what one calls the "center" of the box is
arbitrary. A protein at the "edge" of the box and one at the "center" feel
exactly the same water environment and forces. So be sure you are not wasting
your time doing something that will make no difference.

I suspect that some combination of the translate and image commands, with
imaginative choice of options, might be able to do what you describe. Don't
be afraid to experiment.


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Received on Tue Jul 03 2018 - 06:00:03 PDT
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