Re: [AMBER] Can we solvate the box with ligand

From: David A Case <>
Date: Fri, 24 Jan 2014 10:57:48 -0500

On Fri, Jan 24, 2014, Ayesha Fatima wrote:

> I am looking for any one who can tell me whether it is possible to solvate
> the box with ligand along with water molecules.

> I am actually interested learning the
> effect of concentration on protein ligand complexation with the idea that
> the effect of ligand is concentration dependent.

Amber's commands are not very helpful for this sort of problem. The packmol
program is often used to create complex environments: use it to build a box
with components you want, save that as a PDB file, then use loadPdb to get
that into LEaP. Use the "set box" command to get the box size information
imported, since that is not in the PDB file.

Tutorial A15 gives an illustration of using packmol, but there are other good
learning tools as well.


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Received on Fri Jan 24 2014 - 08:00:02 PST
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