Hi,
Use the GitHub version of cpptraj (which does not have this issue):
https://github.com/Amber-MD/cpptraj
-Dan
On Wed, Mar 6, 2019 at 12:21 PM Rosellen, Martin
<martin.rosellen.16.ucl.ac.uk> wrote:
>
> 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 Mon Mar 11 2019 - 12:30:03 PDT
