Re: [AMBER] Creating a new Solvatebox

From: David A. Case <>
Date: Mon, 22 Jul 2013 18:49:17 -0400

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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Received on Mon Jul 22 2013 - 16:00:02 PDT
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