Re: [AMBER] residual dipolar coupling restraints

From: case <>
Date: Wed, 1 Jun 2011 22:09:21 -0400

On Wed, Jun 01, 2011, Brendan Duggan wrote:

> 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.

I'll take a look at this: it's pretty trivial to change the
makeDIP_RST.protein, etc. scripts. Not sure why they didn't get updated with
the ones used to create the files in the test directory.

> In this posting ( 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?

I think you are misreading the namelist input, e.g.:

   ndip=66, dcut=-1.0, dwt=66*0.1,
   gigj = 50*7.847, 8*-3.163, 8*7.847,
   s11=-14.357, s22=-18.844, s12=1.286, s13=-29.811, s23=-44.361,
   id(1)=9, jd(1)=10, dobsl(1)= 4.39, dobsu(1)= 4.39,
   id(2)=42, jd(2)=43, dobsl(2)= 9.81, dobsu(2)= 9.81,

Here "dwt" is an array, with 66 elements, each equal to 0.1; gigj is also
a 66-member array: the first 50 values are 7.847 (meaning that the first 50
entries are C-H dipolar couplings), etc. It is *not* the case
that dwt is a single value of 6.6.

> 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?

Hope the above helps: each peak (numbered 1-66 in this example) has associated
with it values of dwt, gigj, id, jd, dobsl and dobsu.

> 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.

The nuclear "g" factors are g_N, and are dimensionless. beta_N is the nuclear
Bohr magneton (

...good luck....dac

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Received on Wed Jun 01 2011 - 19:30:02 PDT
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