Re: [AMBER] AddToBox Failure

From: David Case <>
Date: Wed, 3 May 2017 13:20:16 -0400

On Wed, May 03, 2017, sylvester kisembo wrote:

> 1. I Re-run the AddToBox command with your recommendations and it still
> failed. The entire output is in the file called "output".

OK: easy to see the problem. Your box dimensions (specified in the CRYST1
record in Limone1.pdb) are 1x1x1 Ang. You are asking AddToBox to add
molecules to a tiny box.

But further, since what you are trying to add is a 30-atom molecule, AddToBox
is probably not a best solution: it was build to add smallish molecules, like
water and monoatomic ions, to biomolecules. It looks like you are trying
to build a molecular liquid; for this the "packmol" program is better suited.

If you do want to use AddToBox, you need to specify the box size you want
in the CRYST1 record in the input pdb file.

...good luck....dac

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Received on Wed May 03 2017 - 10:30:03 PDT
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