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
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Received on Sat Jul 01 2017 - 11:00:03 PDT
