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
Hi Dan
I added the "debug actions 1" statement to my cpptraj input file and played around with various entries in the Karplus.txt file. The lines I would like to include and tested are as follows:
# Values taken from Schmidt et al 1999 J. Biomol NMR 14 pp1-12
C H N CA HA 7.09 -1.05 0.65
ALA ARG ASP ASN ASH CYS CYX GLN GLU HID HIE HIP ILE LEU LYS MET PHE SER THR TRP TYR VAL
When processing a Karplus.txt file that includes the entry above cpptraj produced no jcoupling file and prints to stderr this message
Error: jcoupling::setup: Atom H :0 not found for residue 0
The first residue in my protein is a lysine. If I remove LYS from my entry in the Karplus.txt file it processes successfully. I tried adding entries similar to mine where the H was replaced with H1, H2 or H3, but cpptraj produces the same error and no jcoupling output. It seems that when cpptraj can't find an atom used in a torsion definition it doesn't produce any jcoupling output at all, even though it is still possible to measure other torsions.
The coupling I am trying to extract from my trajectory is a pretty standard one measured by NMR. It would be nice if cpptraj didn't choke on the missing H atom at the N-terminus.
Brendan
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Received on Tue Jun 04 2013 - 12:00:02 PDT
