[AMBER] residual dipolar coupling restraints

From: Brendan Duggan <bmduggan.musc.edu>
Date: Wed, 1 Jun 2011 16:14:15 -0400

I have just started trying to use some residual dipolar coupling restraints
to refine a protein structure and am having trouble generating the restraint

I used makeDIP_RST.protein and it created a file with dobs instead of dobsl
and dobsu. I corrected the output with a script but it would be nice if the
correct format was generated initially.

In this posting (http://archive.ambermd.org/200910/0261.html) and in the
RST.dip, RST.dip2 and RST.dip3 files found in amber11/test/rdc dwt appears
to be scaled by the number of restraints, as is gigj, but this is not
mentioned in the manual. Is this required or just a good idea?

The test files also seem to use several values of gigj, presumably for
different types of RDCs. How are the different values of gigj linked to the
restraints that come later in the namelist?

Under the gigj description the manual gives a formula but its not clear to
me if the 'nuclear "g factors' mentioned are gammaN or gN in the formula, or
what betaN is.

Thanks for any pointers.

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Received on Wed Jun 01 2011 - 13:30:03 PDT
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