Hi,
On Fri, May 31, 2013 at 4:03 PM, Duggan, Brendan <bmduggan.ucsd.edu> wrote:
> Using Karplus parameters in "/opt/amber12/dat/Karplus.txt"
> 195 parameters found for 32 residues.
>From this, I assume you are using your modified Karplus.txt (the
default one has 195 parameters for 24 residues). What happens if you
use the default parameters?
> Also note how cpptraj is looking at residues with numbers outside of those given by the mask.
This warning/behavior is expected. By default cpptraj attempts to
assign parameters for every residue; parameters are only skipped if
not all atoms for that residue parameter set are selected. This
probably could be made more efficient.
I would say as a first try just use the default parameters and see if
the residue recognition problem goes away; that will give us a good
starting point. Also, if you run with 'debug actions 1' set prior to
your jcoupling command the entire list of loaded parameters will be
written to STDOUT; you can check that to see if anything looks off. If
you're still having trouble you can send me the Karplus.txt file you
made and I can see if I can get the same behavior.
-Dan
--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-9119 (Fax)
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Received on Fri May 31 2013 - 15:30:03 PDT
