Re: [AMBER] Creating a new Solvatebox

From: Chinthaka Ratnaweera <>
Date: Mon, 22 Jul 2013 19:52:45 -0500

Thank you Dr Case

Can you please clarify me these

Once the saveoff command make a box 'unit' ( I guess I have to save it as
a lib file), inorder to use that unit to solvate the protein, do I have to
use loadoff command to open it and give this unit name as second argument
in solvatebox command?

Does size of the solvate box matters when setup the initial box using


On Mon, Jul 22, 2013 at 5:49 PM, David A. Case <>wrote:

> On Mon, Jul 22, 2013, Chinthaka Ratnaweera wrote:
> > Can a user create a new solvatebox for a solvent which is not already
> > included in amber (e.g. solvate box for methanol is there but not for
> > ethanol). If so can anyone guide me how to do that.
> It's probably simplest to use packmol to set up an initial box; save it as
> a PDB file, then load that pdb file into tleap to set up the amber prmtop
> and
> coordinates; then equilibrate to get a good temperature and density; then
> reload back into tleap and use the saveoff command to make a box "unit".
> Tutorial A15 can show you a lot of this, although we did not do the final
> step
> there of making the off file.
> ...good luck...dac
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Chinthaka Nadun Ratnaweera
Hand Lab Rm 1126
Mississippi State University
310 Presidents Circle
Starkville, MS 39762
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Received on Mon Jul 22 2013 - 18:00:02 PDT
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