On Thu, May 23, 2013 at 11:28 AM, Duggan, Brendan <bmduggan.ucsd.edu> wrote:
> Using Karplus parameters in "/opt/amber12/dat/Karplus.txt"
This indicates you are using the default parameter file
($AMBERHOME/dat/Karplus.txt). You can add your parameters to that
file. Currently, the way the code is set up it will always use that
file if it is found. You can currently point it to a custom file by
unsetting AMBERHOME and setting an environment variable KARPLUS with
the absolute path to your custom parameter file. A future update will
make this process a bit easier.
-Dan
Actually, the file $AMBERHOME/dat/Karplus.txt is the one I created and that cpptraj does not like. My installation did not include a Karplus.txt file in $AMBERHOME/dat. Do you have a Karplus.txt file that works and that you could send me?
Brendan
Thanks for the Karplus.txt file Dan, it seems to be working fine and I can add my own parameters to it that are recognised by cpptraj. Now, however, I am having problems with the jcoupling statement processing the mask. In the output below you can see that in the input section the jcoupling statement reads parameters from the Karplus.txt file for 32 residues, however it can't seem to match those with some of the residues in the trajectory. Specifically it does not find ALA, CYX, GLY, SER, THR, TYR, VAL. My protein does not have Trp or any His variants other than HIE so I have not tested those, but the other standard residues it finds fine. Also note how cpptraj is looking at residues with numbers outside of those given by the mask.
If you have any suggestions for what I am doing wrong I would appreciate hearing them.
CPPTRAJ: Trajectory Analysis. V13.1
___ ___ ___ ___
| \/ | \/ | \/ |
_|_/\_|_/\_|_/\_|_
INPUT: Reading Input from file jcoup.cpptraj
[parm ../protein.prmtop]
AmberParm Title: [default_name]
Radius Set: modified Bondi radii (mbondi)
[trajin ../production.nc]
[production.nc] contains 50000 frames.
[jcoupling :1-85 outfile protein.jcoupling]
J-COUPLING: Searching for dihedrals in mask [:1-85].
Using Karplus parameters in "/opt/amber12/dat/Karplus.txt"
195 parameters found for 32 residues.
Writing output to protein.jcoupling
.
snipped
.
BEGIN TRAJECTORY PROCESSING:
.....................................................
ACTION SETUP FOR PARM [napc2.Na+WAT.prmtop] (1 actions):
0: [jcoupling :1-85 outfile protein.jcoupling]
Warning: Jcoupling::setup: Karplus parameters not found for residue [2:ALA ]
Warning: Jcoupling::setup: Karplus parameters not found for residue [3:THR ]
Warning: Jcoupling::setup: Karplus parameters not found for residue [6:CYX ]
Warning: Jcoupling::setup: Karplus parameters not found for residue [7:GLY ]
Warning: Jcoupling::setup: Karplus parameters not found for residue [12:TYR ]
Warning: Jcoupling::setup: Karplus parameters not found for residue [14:SER ]
Warning: Jcoupling::setup: Karplus parameters not found for residue [15:CYX ]
Warning: Jcoupling::setup: Karplus parameters not found for residue [16:GLY ]
Warning: Jcoupling::setup: Karplus parameters not found for residue [17:SER ]
Warning: Jcoupling::setup: Karplus parameters not found for residue [20:CYX ]
Warning: Jcoupling::setup: Karplus parameters not found for residue [24:CYX ]
Warning: Jcoupling::setup: Karplus parameters not found for residue [26:TYR ]
Warning: Jcoupling::setup: Karplus parameters not found for residue [28:GLY ]
Warning: Jcoupling::setup: Karplus parameters not found for residue [29:VAL ]
Warning: Jcoupling::setup: Karplus parameters not found for residue [39:VAL ]
Warning: Jcoupling::setup: Karplus parameters not found for residue [41:CYX ]
Warning: Jcoupling::setup: Karplus parameters not found for residue [43:VAL ]
Warning: Jcoupling::setup: Karplus parameters not found for residue [45:VAL ]
Warning: Jcoupling::setup: Karplus parameters not found for residue [46:CYX ]
Warning: Jcoupling::setup: Karplus parameters not found for residue [50:CYX ]
Warning: Jcoupling::setup: Karplus parameters not found for residue [51:VAL ]
Warning: Jcoupling::setup: Karplus parameters not found for residue [52:CYX ]
Warning: Jcoupling::setup: Karplus parameters not found for residue [55:GLY ]
Warning: Jcoupling::setup: Karplus parameters not found for residue [57:TYR ]
Warning: Jcoupling::setup: Karplus parameters not found for residue [64:CYX ]
Warning: Jcoupling::setup: Karplus parameters not found for residue [65:VAL ]
Warning: Jcoupling::setup: Karplus parameters not found for residue [66:SER ]
Warning: Jcoupling::setup: Karplus parameters not found for residue [67:ALA ]
Warning: Jcoupling::setup: Karplus parameters not found for residue [70:CYX ]
Warning: Jcoupling::setup: Karplus parameters not found for residue [79:TYR ]
Warning: Jcoupling::setup: Karplus parameters not found for residue [81:GLY ]
Warning: Jcoupling::setup: Karplus parameters not found for residue [82:THR ]
Warning: Jcoupling::setup: Karplus parameters not found for residue [86:Na+ ]
Warning: Jcoupling::setup: Karplus parameters not found for residue [87:Na+ ]
Warning: Jcoupling::setup: Karplus parameters not found for residue [88:Na+ ]
Warning: Jcoupling::setup: Karplus parameters not found for residue [89:Na+ ]
Warning: Jcoupling::setup: Karplus parameters not found for residue [90:Na+ ]
Warning: Jcoupling::setup: Karplus parameters not found for residue [91:Na+ ]
Warning: Jcoupling::setup: Karplus parameters not found for residue [92:Na+ ]
Warning: Jcoupling::setup: Karplus parameters not found for residue [93:Na+ ]
Warning: Jcoupling::setup: Karplus parameters not found for residue [94:Na+ ]
Warning: Jcoupling::setup: Karplus parameters not found for residue [95:Na+ ]
Warning: Jcoupling::setup: Karplus parameters not found for residue [96:Na+ ]
Warning: Jcoupling::setup: Karplus parameters not found for residue [97:Na+ ]
J-COUPLING: [:1-85] Will calculate J-coupling for 385 dihedrals.
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Received on Fri May 31 2013 - 15:30:02 PDT
