I have been trying to get the jcoupling command in cpptraj to work without success. Does anyone have an example Karplus.txt file they would be willing to share? I have tried constructing my own following the specifications in the manual and came up with the following:
C H N CA HA 7.90 -1.05 0.65
ALA ARG ASN ASP CYS CYX GLU GLN HID HIE HIS ILE LEU LYS MET PHE PRO SER THR TRP TYR VAL
C H N CA HA2 7.90 -1.05 0.65
GLY
but it produces no output. Here is the relevant information produced when running cpptraj.
[jcoupling :1-85.H,N,CA,HA outfile napc2.jcoupling]
J-COUPLING: Searching for dihedrals in mask [:1-85.H,N,CA,HA].
Using Karplus parameters in "/opt/amber12/dat/Karplus.txt"
23 parameters found for 23 residues.
Writing output to napc2.jcoupling
10: [jcoupling :1-85.H,N,CA,HA outfile napc2.jcoupling]
Warning: Setup failed for [jcoupling :1-85.H,N,CA,HA outfile napc2.jcoupling]: Skipping
Brendan M. Duggan, PhD
NMR Facility Director and Associate Project Scientist
Skaggs School of Pharmacy and Pharmaceutical Sciences
University of California at San Diego
9500 Gilman Drive, MC 0684
La Jolla CA 92093
office phone: (858) 534-8763
lab phone: (858) 822-7826
cell phone: (858) 692-2298
email: bmduggan.ucsd.edu
http://sopnmr.ucsd.edu
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Received on Thu May 23 2013 - 11:00:02 PDT
