AMBER Archive (2008)

Subject: Re: AMBER: solvent box again

From: David A. Case (case_at_biomaps.rutgers.edu)
Date: Tue Dec 16 2008 - 14:02:05 CST

On Tue, Dec 16, 2008, iccy liu wrote:
>
>
> I build a box size of 20Ax20Ax20A with my solvent molecule, and then run
> MD in NVT ensemble to relax it. I did min and heat it up to 300K step
> wise. Later I extracted my final structure, I found out that the shape of
> my solvent box is not a cub anymore.

As Ross said, you probably need to use the "image" command in ptraj.

> My question is now: how to solvate my system with my solvent box? what
> keyword to use? I am very new to Amber. In fact, I still did not figure out
> how to solvate my system with a single molecule as Professor Case mentioned
> in his reply.

The keyword is "solvateBox" or "solvateOct", described in section 3.4.38 of
the Users' Manual. The second argument can be a single molecule or a
pre-equilibrated box. You need to create a LEaP unit for either of these...
if you have done the MD with your solvent alone, you already shold be most of
the way there.

...dac

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