1. The value of nbxmod is really not that critical. It should probably
have been
4 for the RNA case, but it worked perfectly well with 3. It must have been
because I created
the RNA case from another script. Bottom line, it has nothing to do with
the database
potential stuff. There is no harm in leaving it at 3.
2. To get the calculated rgyr for your structure just type the following:
coor rgyr end
(you can have the option of mass=true or mass=false).
Marius
-----Original Message-----
From: hmertens
To: [email protected]
Sent: 10/9/2003 6:29 PM
Subject: [Xplor-nih] parameter set-up with delphic.
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.
---------------------------
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