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
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
to majordomo.scripps.edu
Received on Wed Jun 18 2008 - 06:07:18 PDT
