AMBER Archive (2008)

Subject: Re: AMBER: Problem with running refinement of NMR structures with RDCs

From: David A. Case (case_at_scripps.edu)
Date: Sun Jun 15 2008 - 20:50:53 CDT

On Sun, Jun 15, 2008, Qi Zhang wrote:
>
> I am trying to refine NMR structures using Amber7 with experimental
> data, and I had a problem when I included RDCs as restraints. The
> Amber refinement ran well with just NOEs, however, when I included
> RDCs, the program kept running for hours without exporting any
> results, kind of looping within the program.
>
> The last part from the output file reads like,
>
> 4. RESULTS
> eedmeth=5: Using 1/r dielectric
> Local SIZE OF NONBOND LIST = 433233
> Total SIZE OF NONBOND LIST = 433233
>
> I have also compiled Amber7 in a recent purchased computer in the lab,
> and the refinement ran through without any problem with both NOE and
> RDCs as restraints. I am wonder is there any specific hardware
> requirement in order to run Amber refinement with RDCs?

I know of no such requirement. If you are getting different results on two
different computers with exactly the same inputs, you may be facing either a
hardware problem or a compiler problem on the failing machine.

...dac

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