Hi,
I am trying to analyse chi1 angles and run into problems with amino acid types not having a 'CG' atom.
Here the command line output from cpptraj for a valine:
---------- RUN BEGIN -------------------------------------------------
PARAMETER FILES (1 total):
0: WT.prmtop, 221576 atoms, 71504 res, box: Trunc. Oct., 70925 mol, 70919 solvent
INPUT TRAJECTORIES (1 total):
0: 'WT.inpcrd' is an AMBER restart file, no velocities, Parm WT.prmtop (Trunc. Oct. box) (reading 1 of 1)
Coordinate processing will occur on 1 frames.
BEGIN TRAJECTORY PROCESSING:
.....................................................
ACTION SETUP FOR PARM 'WT.prmtop' (1 actions):
0: [multidihedral chip resrange 241 out VAL241.xvg]
Warning: No dihedrals selected for topology WT.prmtop
Warning: Setup incomplete for [multidihedral]: Skipping
----- WT.inpcrd (1-1, 1) -----
100% Complete.
Read 1 frames and processed 1 frames.
TIME: Avg. throughput= 349.6503 frames / second.
ACTION OUTPUT:
DATAFILES (1 total):
VAL241.xvg (XVG file):
Warning: File 'VAL241.xvg' has no sets containing data.
RUN TIMING:
TIME: Init : 0.0000 s ( 0.72%)
TIME: Trajectory Process : 0.0029 s ( 98.32%)
TIME: Action Post : 0.0000 s ( 0.00%)
TIME: Analysis : 0.0000 s ( 0.00%)
TIME: Data File Write : 0.0000 s ( 0.28%)
TIME: Other : 0.0000 s ( 0.01%)
TIME: Run Total 0.0029 s
---------- RUN END ---------------------------------------------------
It works fine for amino acids having a 'CG' atom like found in this table with definitions of chi angles:
http://www.msg.ucsf.edu/local/programs/garlic/commands/dihedrals.html
best
Martin
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Received on Wed Mar 06 2019 - 09:30:02 PST
