Re: [AMBER] EAMBER (non-restraint) in sander output

From: Duggan, Brendan <>
Date: Thu, 19 Jun 2014 21:55:12 +0000

Hi Dave

Thanks for your reply. I was thinking that sander could be changed so that the EAMBER (non-restraint) line would be printed if nmropt > 1. There currently must be a test to see if the restraint energy is greater than zero to print the line. Replacing this with a test for nmropt should not affect too many other things. I would not expect any of the test cases using restraints would have restraints that are not violated, so the test cases would not be altered either. Something to think about.

There are other problems with sviol that I have made some hacks to get around so I will tidy those up and look at avoiding the zero restraint energy issue as well.



Message: 8
Date: Wed, 18 Jun 2014 21:25:07 -0600
From: David A Case <>
Subject: Re: [AMBER] EAMBER (non-restraint) in sander output
To: AMBER Mailing List <>
Message-ID: <>
Content-Type: text/plain; charset=us-ascii

On Wed, Jun 18, 2014, Duggan, Brendan wrote:

> I am running simulated annealing calculations with NMR restraints using
> sander in Amber14 and have discovered that if the restraint energy is 0
> then the line starting with "EAMBER (non-restraint) =" is not included
> in the output. I was wondering if this was intentional? The absence
> of the line results in the violation summary script "sviol" including
> incorrect values in its summary tables. If there is a reason to not
> include the line I can work with that and modify "sviol" to calculate
> the value for EAMBER (non-restraint) but it would be easier if the value
> was already there.

I think at this point changing sviol is likely to be the better route; or,
you can modify your local version of sander to always print out the
non-restraint line. Changing sander for everyone would break every test case
we have. We do have automated scripts to fix the test cases for changes in
output format, but we'll have to think about whether we want to use that
option here.

...thanks for the report...dac
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Received on Thu Jun 19 2014 - 15:00:02 PDT
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