Hi *
Thanks for the tips Charles.
I did tried to run an anneal.py with and without RAMA. And the results
clearly show that the X best structures from the annealing with RAMA do
show a better agreement (rmsd from superposition) between the mainchain
as well as the sidechains on the ensemble. Great!
But I still have one question, about the rama stuff. When I was reading
and trying to understand some scripts using rama
(eg.eginputs/sry/sry_finall.inp), I saw that the torsional database has
3 sets of potentials: the raw (called with xrama), gaussians (called
with rama) and quartics (also called by rama). When I call rama from
python, what set am I using: gaussians or quartic? And am I using short
range (intra-residue) as well as long range (inter-residues)
correlations? I just want to know what I'm doing when adding rama to the
target function.
One more. Reading the article [J. Magn. Res. 146, 249-254 (2000)], the
authors define the DELPHIC torsions database as the original
implementation of the torsion angle potential. So, when talking about
the DELPHIC database, are we talking about the raw potentials or
something else? And if that's the case, then instead of calling rama
should I call xrama instead of rama? Do not forget that I'm calculating
structures in non-aqueous environments.
protocol.initRamaDatabase()
potList.append( XplorPot('XRAMA') )
Cheers,
L.
Charles at Schwieters.org wrote:
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> Hello L?on--
>
>
>> Are the following rama related commands in the anneal.py the correct
>> ones to use the Rama torsion angle database in my case?
>>
>
> yes.
>
>
>> I'm using the anneal.py script (eginput/gb1_rdc) as a template to my
>> calculations, though not using rdc stuff. Commented all RAMA stuff in
>> my first runs.
>>
>
> that should work. Please let us know if you have probelms.
>
> best regards--
> Charles
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