Re: [AMBER] Parameter and coordinate files

From: David A Case <>
Date: Mon, 18 Jan 2016 08:02:08 -0500

On Sun, Jan 17, 2016, Stefano Sarao S215563 wrote:
> I broke the molecule in four pieces but it still gave error. How many
> atoms should I simulate to get a proper result?

I don't remember exactly what your molecule looked like, but it seemed like
there were dozens of nearly identical units. You want fragments that are as
small as possible, yet still contain the functional groups and chemistry that
is important.

Note that stiching things back together will require extra work, beyond that
usually used for parameterizing small molecules. See tutorial B5 to get
started. But your problem will require you to learn what is going on in each
of these steps.

....good luck...dac

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Received on Mon Jan 18 2016 - 05:30:04 PST
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