Re: [AMBER] solvation box

From: David A Case <>
Date: Thu, 9 Nov 2017 07:44:40 -0500

On Thu, Nov 09, 2017, Shilpa Gupta wrote:
> I want to simulate the molecular dynamics simulations of the dendrimer in
> the presence of [bmim][cl] ionic liquid. For this i have generated
> [bmim][cl] box using packmol and equilibrated the box. How do i solvate the
> dendrimer molecule using this box. Or is there another way to generate the
> initial solvated structure of the dendrimer. Thanks in advance.

You should be able to continue using packmol, but Amber's AddToBox program
attacks much the same problem, so you might look into that as well.

I don't know that we have any instructions about how to build a solvent box as
a unit in LEaP. But basically you use loadPdb to load your packmol pdb file,
then use "set unit box..." to make it a peridioc system. I think you then
should be able to use the solvateBox command in LEaP to solvate the dendrimer.

So, you have three choices. Maybe others on the list can comment on applying
these ideas to ionic liquids.


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Received on Thu Nov 09 2017 - 05:00:02 PST
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