On Fri, Aug 20, 2010, Vickie Roberts wrote:
>
> Balvinder Singh (Wed Sep 08 2004 - 15:49:04 PDT)
>
> I have rediscovered this problem in minimizations of 30 complexes
> of 2 proteins that I minimized with the following protocol: initial
> minimiation with strong restraints in vacuo, then with restraints
> using GB, then unrestrained with GB.
Hi Vickie!
If you are planning extensive minimizations to low RMS values, use the xmin
minimizer, which is much better. For examples, see:
$AMBERHOME/AmberTools/test/nab/txmin.nab (for NAB)
$AMBERHOME/test/gb_rna/Run.gbrna.xmin (for sander)
I'm hoping to just scrap the ancient, ancient conjugate gradient minimizer
in some future release. It is enormously complex, and debugging your problem
looks both hard and fruitless: xmin *should* work better and more reliably.
Plus, Istvan understands the code if there is a problem, whereas I don't think
anyone understands the innards of the CG routine.
...good luck....dac
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Received on Fri Aug 20 2010 - 05:00:06 PDT
