Re: [AMBER] RESOLVED: peek_ewald_inpcrd: Box info not found in inpcrd

From: Matias Machado <>
Date: Sun, 16 Sep 2018 12:35:10 -0300 (UYT)

Dear ???,

If there is no box information in your coordinate file, then you have set something wrong during the topology and coordinates generation...

Did you visually inspect the system before running? is the water present? Because the command "solvatebox foo TIP3PBOX 10.0" should add the box information into the system (at the last line in the inpcrd file)...

I'm not an AMBER developer to tell you about the code check points, but without box information (the usual set up for igb>0) you can't apply any pbc condition, so by removing "ntb" you are setting no periodicity (ntb=0, which is the default in igb>0)...

So, removing "ntb" may not be a way to solve the problem but a way to avoid an error message, which indeed means hiding the real problem...

I think this example is a very good reason to keep the ntb flag, so you can really check on what you are doing.

Hence, I think the following statement in the manual may not be complete true:

"There is no longer any need to set this variable, since it can be determined from igb and ntp parameters."

Because if you mess up with the box information then you may end up running at unwanted conditions without knowing...



Researcher at Biomolecular Simulations Lab.
Institut Pasteur de Montevideo | Uruguay

----- Mensaje original -----
Para: "AMBER Mailing List" <>
Enviados: Domingo, 16 de Septiembre 2018 0:24:35
Asunto: [AMBER] RESOLVED: peek_ewald_inpcrd: Box info not found in inpcrd

This error was resolved for sander runs by simply removing the line with
"ntb=1," in the file and the line with "ntb=2," in the file


The User's Manual states that the ntb setting is not really needed anymore,
since other parameters can be used to obtain the information.


However, why doesn't a developer/curator remove the "ntb= ," lines from
these files in the Alanine Leap and MD tutorial.

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Received on Sun Sep 16 2018 - 09:00:02 PDT
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