AMBER Archive (2008)

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

From: Qi Zhang (qizhang_at_mbi.ucla.edu)
Date: Sun Jun 15 2008 - 15:20:21 CDT

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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