Re: [AMBER] Reference structure for targeted MD

From: David Case <>
Date: Tue, 16 May 2017 08:28:30 -0400

On Mon, May 15, 2017, Francesco Gentile wrote:

> I am trying to run a targeted MD simulation. Reading the manual, it says
> that both the reference and the input coordinates should match the prmtop
> file. I am wondering how this can be done, as I don't expect to see the
> same number of water molecules by solvating the two structures, even using
> the same parameters for leap. Thanks in advance for your help,

You will have to fiddle with the two structures to get them to have the same
number of water molecules. You could AddToBox to increase the number of
waters in the one with less (if you have a periodic simulation), or use
trial and error with the buffer you give to tleap to get an equivalent number.

....good luck...dac

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Received on Tue May 16 2017 - 05:30:04 PDT
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