Hi,
I think the issue here is that you are loading your topology on the
command line, but then also loading it in your script and giving it a
tag ([cpu]). Try just running:
cpptraj -i pca-cpu-gpu.cpptraj
Does that help?
-Dan
On Sat, Jul 1, 2017 at 1:40 PM, Marcelo Andrade Chagas
<andrade.mchagas.gmail.com> wrote:
> Dear Community Users of AMBER,
>
> I need to do a PCA analysis.
>
> I got the following error in cpptraj.
>
> From what I noticed this is related to creating a file.
>
> This file is created from which output files
> Of simulation and how?
>
> Regards,
>
> Marcelo
>
> use tutorial
>
> http://www.amber.utah.edu/AMBER-workshop/London-2015/pca/
>
> marcelo.marcelo:~/TRABALHO-ADOLFO/TRABALHO-I-ADOLFO/ARQUIVOS-DM-PROT-II/DM-5GOZ/ANALISE/TESTE-PCA/TESTE-PCA-II/PCA-TESTE-II/PCA-TESTE-III$
> cpptraj -i pca-cpu-gpu.cpptraj -p proteina.prmtop
>
> CPPTRAJ: Trajectory Analysis. V16.16
> ___ ___ ___ ___
> | \/ | \/ | \/ |
> _|_/\_|_/\_|_/\_|_
>
> | Date/time: 07/01/17 14:34:04
> | Available memory: 3.810 GB
>
> Reading 'proteina.prmtop' as Amber Topology
> INPUT: Reading input from 'pca-cpu-gpu.cpptraj'
> [parm proteina.prmtop [cpu]]
> Reading 'proteina.prmtop' as Amber Topology
> [trajin proteina.mdcrd parm [cpu]]
> Reading 'proteina.mdcrd' as Amber NetCDF
> [rms first :1-262&!.H=]
> RMSD: (:1-262&!.H*), reference is first frame (:1-262&!.H*).
> Best-fit RMSD will be calculated, coords will be rotated and translated.
> [average crdset AVG]
> Setting active reference for distance-based masks: 'AVG'
> AVERAGE: Averaging over coordinates in mask [*]
> Start: 1 Stop: Final frame
> Saving averaged coords to set 'AVG'
> [createcrd proteina-trajectories]
> CREATECRD: Saving coordinates from Top proteina.prmtop to
> "proteina-trajectories"
> [run]
> ---------- RUN BEGIN -------------------------------------------------
>
> PARAMETER FILES (2 total):
> 0: proteina.prmtop, 4086 atoms, 262 res, box: Orthogonal, 1 mol
> 1: [cpu] proteina.prmtop, 4086 atoms, 262 res, box: Orthogonal, 1 mol
>
> INPUT TRAJECTORIES (1 total):
> 0: 'proteina.mdcrd' is a NetCDF AMBER trajectory, Parm proteina.prmtop
> (Orthogonal box) (reading 534 of 534)
> Coordinate processing will occur on 534 frames.
>
> REFERENCE FRAMES (1 total):
> 0: AVG
> Active reference frame for distance-based masks is 'AVG'
>
> BEGIN TRAJECTORY PROCESSING:
> .....................................................
> ACTION SETUP FOR PARM 'proteina.prmtop' (3 actions):
> 0: [rms first :1-262&!.H=]
> Target mask: [:1-262&!.H*](2039)
> Reference mask: [:1-262&!.H*](2039)
> Warning: Coordinates are being rotated and box coordinates are present.
> Warning: Unit cell vectors are NOT rotated; imaging will not be possible
> Warning: after the RMS-fit is performed.
> 1: [average crdset AVG]
> Mask [*] corresponds to 4086 atoms.
> Averaging over 4086 atoms.
> 2: [createcrd proteina-trajectories]
> Error: # atoms in current topology (4086) != # atoms in coords set
> "proteina-trajectories" (0)
> Error: Setup failed for [createcrd]
> Warning: Could not set up actions for proteina.prmtop: skipping.
> Read 0 frames and processed 0 frames.
> TIME: Avg. throughput= 0.0000 frames / second.
>
> ACTION OUTPUT:
>
> DATASETS (2 total):
> RMSD_00002 "RMSD_00002" (double, rms), size is 0
> proteina-trajectories "proteina-trajectories" (coordinates), size is 0
> (0.024 kB) 0 atoms
>
> RUN TIMING:
> TIME: Init : 0.0000 s ( 1.96%)
> TIME: Trajectory Process : 0.0012 s ( 75.27%)
> TIME: Action Post : 0.0000 s ( 0.00%)
> TIME: Analysis : 0.0000 s ( 0.00%)
> TIME: Data File Write : 0.0000 s ( 2.28%)
> TIME: Other : 0.0003 s ( 0.20%)
> TIME: Run Total 0.0016 s
> ---------- RUN END ---------------------------------------------------
> [crdaction proteina-trajectories rms ref AVG :1-262&!.H=]
> Using set 'proteina-trajectories'
> Error: trajectory contains no frames.
> 1 errors encountered reading input.
> TIME: Total execution time: 0.0959 seconds.
> Error: Error(s) occurred during execution.
>
> Marcelo Andrade Chagas, MSc
> (PhD student)
> Laboratório de Química Computacional e Modelagem Molecular - LQC-MM
> * http://lqcmm.qui.ufmg.br/
> Departamento de Química da Universidade Federal de Minas Gerais - UFMG
> Tel:(31)3409-5776
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
--
-------------------------
Daniel R. Roe
Laboratory of Computational Biology
National Institutes of Health, NHLBI
5635 Fishers Ln, Rm T900
Rockville MD, 20852
https://www.lobos.nih.gov/lcb
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Received on Mon Jul 03 2017 - 07:00:02 PDT
