Many thanks for the clarification. I had indeed missed the point that dwt
and gigj are arrays. It all makes sense now and I have been able to get a
simulation running. Thanks for your help.
brendan
On Wed, Jun 1, 2011 at 10:09 PM, case <case.biomaps.rutgers.edu> wrote:
> 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 (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?
>
> I think you are misreading the namelist input, e.g.:
>
> &align
> 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 (http://en.wikipedia.org/wiki/Nuclear_magneton).
>
> ...good luck....dac
>
>
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Received on Tue Jun 07 2011 - 07:30:02 PDT
