Dear Amber users,
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? The computer
that has this problem has the following setting:
Machine type: x86
OS name: Linux
OS release: 2.6.9-42.0.2.ELsmp
CPU speed: 2.4MHz
Memory: 2.0GB
Thank you all for help and suggestion.
Qi
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Received on Wed Jun 18 2008 - 06:07:14 PDT
