Re: [AMBER] Normal Model Analysis with AmberTools20

From: David A Case <>
Date: Thu, 10 Sep 2020 09:31:19 -0400

On Wed, Sep 09, 2020, Harley Wilson wrote:
>With the manual, I do not understand these lines of code and what they do
>(pg. 839):
> $ molecule m
> $ float x[4000], fret

These are not lines that you type at the command line; they are text that
would be part of a nab program.

To get started, look at the sample programs in
$AMBERHOME/AmberTools/test/nabc, especially tnmode.c. You would have to first
create a prmtop and rst7 file for your system, then compile tnmode.c (see the
Makefile, and type "make tnmode"), then run the program.

Start with a *much* smaller molecule or peptide to learn from. Normal mode
calculations on full proteins can take a lot of time and memory, so start with
smaller systems first.

...good luck....dac

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Received on Thu Sep 10 2020 - 07:00:03 PDT
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