Re: [AMBER] How to move the protein to the corner of the box.

From: David A Case <>
Date: Sun, 20 Aug 2017 09:05:52 -0400

On Sat, Aug 19, 2017, Parviz Seifpanahi Shabane wrote:

> I want to move my protein to the corner of the box to make it smaller, I am
> interested dynamics of just one part of the proteins and I will put
> restoration another part on a fix in the corner, I used the "translate"
> command but it seems it does not work. any suggestions? this my leap script

Remember that you have a periodic system, so it really doesn't make any
difference whether the protein is in the "corner" of the box or in the
"center". (But maybe I am not understanding your question or desire.)

> solvateBox mol OPCBOX 4 iso
> translate mol {3 3 0}

Here "mol" is the entire system, protein + water. So you are translating
the entire periodic system, which changes nothing: the absolute position
of the unit cell in space is irrelevant.

...hope this helps...dac

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Received on Sun Aug 20 2017 - 06:30:03 PDT
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