Hello everyone,
I was wondering if anyone can clear this up for me. I have noticed that
in some of the example scripts a different value for nbxmod is declared
even though the DELPHIC potentials are used in all of these cases. In
the mef_dna example:
==> nbxmod 4 {* This is 4, because we are using database
(delphic) *}
{*
potentials. *}
In the dna example:
==> nbxmod=4 {*With internal dynamics and the database potential,
nbxmod should be 4. *}
but in the RNA refinement example (with the database potentials declared):
==> nbxmod=3 .
I think I'm getting a little confused. Is the basic rule that the
DELPHIC terms refine 3 bond interactions, thus it must be set to 4
bonds? Is the RNA example a little different? Should nbxmod=4 if
internal dynamics are being used but the DELPHIC terms are off?
Also, I've been trying to report the "calculated" radius of gyration
and haven't as yet succeeded in getting this in my output analysis.
Can someone please help me out with this too?
I look forward to any handy hints you may have,
Best regards,
Haydyn
--
--------------------------
Haydyn Mertens
PhD student
Dept. Biochem.
Univeristy of Melbourne
Australia.
---------------------------
