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

From: David A Case <>
Date: Wed, 18 Jun 2014 21:25:07 -0600

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

David A. Case                         |   
Dept. of Chemistry & Chemical Biology |
Rutgers University                    | office:   +1-848-445-5885
174 Frelinghuysen Road, Rm. 208b      | cell:     +1-609-651-6817
Piscataway, NJ 08854        USA       |
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Received on Wed Jun 18 2014 - 20:30:02 PDT
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