Re: [AMBER] Tutorial A26: error in reading nameless control

From: Jason Swails <>
Date: Mon, 2 Nov 2015 09:17:45 -0500

On Mon, Nov 2, 2015 at 9:13 AM, Ruth Helena Tichauer <>

> Dear David,
> Thank you a lot for the answer!
> I’m running sander with the following command:
> $AMBERHOME/exe/sander -i -p ala.asmd.prmtop -c ala.asmd_ht.rst
> -ref ala.asmd_ht.rst -o ala.asmd_den.out -r ala.asmd_den.rst -x
> &
> When typing the command “$AMBERHOME/update_amber —version” I have no
> answer (I guess update_amber is not in that directory) but I think that
> amber 11 is the version installed in the computer I use as “$AMBERHOME"
> stands for "/opt/amber11-gnu/."

​Amber 11 is a very old version of Amber (from ~2010) that pre-dates
update_amber as well as the barostat keyword. I would recommend updating
to AmberTools 15, which you can install in your home directory without root
privileges and which includes sander.

> I tried again to run the density equilibration step of tutorial A26, first
> with barostat=1 in the input file which lead to the same error message,
> then, I removed this functionality, and it worked (or at least the MD
> production is running for now). Is it “useful” to do the density
> equilibration step of the system if the pressure regulation isn’t available
> in the amber version I use?

​The 'barostat' keyword was introduced as a way to select between the
Berendsen barostat and the newly-implemented Monte Carlo barostat. In
versions before Amber 14, the only available barostat was Berendsen, and
the "barostat" keyword did not exist.

So as long as you set ntp=1 and ntb=2 in your input file, the system will
equilibrate its density, even if the barostat keyword isn't supported.


Jason M. Swails
Rutgers University
Postdoctoral Researcher
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Received on Mon Nov 02 2015 - 06:30:04 PST
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