Hi,
> Error: Tokenize: Wrong syntax [.]
Like the error said: you used the wrong syntax to select atoms
.CA,N,C should be changed to .CA,N,C
Please double-check manual for the syntax.
(Or have a quick look here:
http://parmed.github.io/ParmEd/html/amber.html?highlight=syntax#amber-mask-syntax
)
cheers.
Hai
On Sat, Oct 22, 2016 at 4:42 AM, Saman Yousuf ali <
saman.yousufali64.yahoo.com> wrote:
> Dear All,I would like to plot ligand rmsd and active site rmsd (residue
> 5A around bound ligand). I used the following script for calculating ligand
> rmsd through out simulation;parm complex.prmtop
> trajin reimaged_complex.mdcrd
> rms :536 first out lig-rmsd.dat
> strip :WAT
> strip :Na+job processed finely and got ligand rmsd plot, but I do not
> whether the above pasted script is correct or not. I have also tried to
> plot active site 5 angstroms rmsd using script pasted below;parm
> complex.prmtop
> trajin reimaged_complex.mdcrd
> rms first out 536-5ang.dat :536<:5.0&.CA,N,C
> strip :WAT
> strip :Na+But I got following errorzuh.node14:~/Working/sya/ptr1/4cm6/complex/min/equ/md>
> cpptraj -i 2.in
>
> CPPTRAJ: Trajectory Analysis. V15.00
> ___ ___ ___ ___
> | \/ | \/ | \/ |
> _|_/\_|_/\_|_/\_|_
>
> | Date/time: 10/22/16 13:31:52
> | Available memory: 266.293 MB
>
> INPUT: Reading Input from file 2.in
> [parm complex.prmtop]
> Reading 'complex.prmtop' as Amber Topology
> [trajin reimaged_complex.mdcrd]
> Reading 'reimaged_complex.mdcrd' as Amber Trajectory
> [rms first out 536-5ang.dat :536<:5.0&.CA,N,C]
> Error: Tokenize: Wrong syntax [.]
> Error: Tokenize: Wrong syntax [.]
> RMSD: (:536<:5.0&.CA,N,C), reference is first frame
> (:536<:5.0&.CA,N,C), with fitting.
> [strip :WAT]
> STRIP: Stripping atoms in mask [:WAT]
> [strip :Na+]
> STRIP: Stripping atoms in mask [:Na+]
> ---------- RUN BEGIN -------------------------------------------------
>
> PARAMETER FILES:
> 0: 'complex.prmtop', 64964 atoms, 19480 res, box: Orthogonal, 18948 mol,
> 18930 solvent, 5000 frames
>
> INPUT TRAJECTORIES:
> 0: 'reimaged_complex.mdcrd' is an AMBER trajectory, Parm complex.prmtop
> (Orthogonal box) (reading 5000 of 5000)
> Coordinate processing will occur on 5000 frames.
> TIME: Run Initialization took 0.0001 seconds.
>
> BEGIN TRAJECTORY PROCESSING:
> .....................................................
> ACTION SETUP FOR PARM 'complex.prmtop' (3 actions):
> 0: [rms first out 536-5ang.dat :536<:5.0&.CA,N,C]
> Error: Could not parse mask [:536<:5.0&.CA,N,C].
> Warning: Setup failed for [rms first out 536-5ang.dat :536<:5.0&.CA,N,C]:
> Skipping
> 1: [strip :WAT]
> Stripping 56790 atoms.
> Stripped parm: 'complex.prmtop', 8174 atoms, 550 res, box:
> Orthogonal, 18 mol
> 2: [strip :Na+]
> Stripping 12 atoms.
> Stripped parm: 'complex.prmtop', 8162 atoms, 538 res, box:
> Orthogonal, 6 mol
> ----- reimaged_complex.mdcrd (1-5000, 1) -----
> 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
>
> Read 5000 frames and processed 5000 frames.
> TIME: Trajectory processing: 266.9376 s
> TIME: Avg. throughput= 18.7310 frames / second.
>
> ACTION OUTPUT:
>
> DATASETS:
> 1 data set:
> RMSD_00000 "RMSD_00000" (double, rms), size is 0
>
> DATAFILES:
> 536-5ang.dat (Standard Data File): RMSD_00000
> Warning: Set 'RMSD_00000' contains no data.
> Warning: File '536-5ang.dat' has no sets containing data.
> ---------- RUN END ---------------------------------------------------
> TIME: Total execution time: 267.7264 seconds.
> ------------------------------------------------------------
> --------------------
> To cite CPPTRAJ use:
> Daniel R. Roe and Thomas E. Cheatham, III, "PTRAJ and CPPTRAJ: Software for
> Processing and Analysis of Molecular Dynamics Trajectory Data". J. Chem.
> Theory Comput., 2013, 9 (7), pp 3084-3095.
>
> Anyone can explain this to me please?
>
> Best,
> Saman Yousuf Ali
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> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Sun Oct 23 2016 - 10:30:03 PDT
