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

From: Bill Ross <>
Date: Mon, 2 Jul 2018 18:58:11 -0700

Why do you want it uncentered?

I think you will need creative means, i.e. make a centered box big
enough to enclose what you want, savepdb, then write a script (awk,
perl, etc) to remove the waters you don't like, load the resulting pdb,
and add use setbox in leap to add a box again.


On 7/2/18 6:15 PM, Jinfeng Chen wrote:
> Hello amber users:
> I got some trouble when using the tleap to generate the topology files.
> I want to create a cubic box, and make the protein somewhere other than the
> center of the box , but either the Solvatebox or Set box give some
> description about this, I wonder if I can make it in tleap. What should I
> use to specify the protein position in the cubic box?
> Any suggestion would be appreciated.
> Thank you.
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Received on Mon Jul 02 2018 - 19:00:02 PDT
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