Dear
I was able to evolve more world the command suggested.
However, the following error appeared in the second step, as
Shown below
Can you tell me what I should change about it?
Best regards
Marcelo
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/TSTE-PCA-IV$
cpptraj -i pca-cpu-gpu.cpptraj
CPPTRAJ: Trajectory Analysis. V16.16
___ ___ ___ ___
| \/ | \/ | \/ |
_|_/\_|_/\_|_/\_|_
| Date/time: 07/03/17 13:35:47
| Available memory: 3.952 GB
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 (1 total):
0: [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]
Estimated memory usage (534 frames): 26.196 MB
----- proteina.mdcrd (1-534, 1) -----
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
Read 534 frames and processed 534 frames.
TIME: Avg. throughput= 6141.8844 frames / second.
ACTION OUTPUT:
AVERAGE: 534 frames, COORDS set 'AVG'
DATASETS (2 total):
RMSD_00001 "RMSD_00001" (double, rms), size is 534
proteina-trajectories "proteina-trajectories" (coordinates), size is
534 (26.196 MB) Box Coords, 4086 atoms
RUN TIMING:
TIME: Init : 0.0000 s ( 0.05%)
TIME: Trajectory Process : 0.0869 s ( 98.67%)
TIME: Action Post : 0.0008 s ( 0.93%)
TIME: Analysis : 0.0000 s ( 0.00%)
TIME: Data File Write : 0.0001 s ( 0.06%)
TIME: Other : 0.0003 s ( 0.00%)
TIME: Run Total 0.0881 s
---------- RUN END ---------------------------------------------------
[crdaction proteina-trajectories rms ref AVG :1-262&!.H=]
Using set 'proteina-trajectories'
----- proteina-trajectories (1-534, 1) -----
RMSD: (:1-262&!.H*), reference is "AVG" (:1-262&!.H*).
Best-fit RMSD will be calculated, coords will be rotated and translated.
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.
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
TIME: Total action execution time: 0.0443 seconds.
[crdaction proteina-trajectories matrix covar name cpu-gpu-covar
:1-262&!.H=]
Using set 'proteina-trajectories'
----- proteina-trajectories (1-534, 1) -----
MATRIX: Calculating covariance matrix, output is by atom.
Matrix data set is 'cpu-gpu-covar'
Start: 1 Stop: Final frame
Mask1 is ':1-262&!.H*'
Mask [:1-262&!.H*] corresponds to 2039 atoms.
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
TIME: Total action execution time: 12.7291 seconds.
[runanalysis diagmatrix cpu-gpu-covar out cpu-gpu-evecs.dat vecs 3 name
myEvecs nmwiz nmwizvecs 3 nmwizfile dna.nmd nmwizmask :1-262&!.H=]
Mask [:1-262&!.H*] corresponds to 2039 atoms.
nmwiz topology 2039 atoms, 262 res, box: Orthogonal, 0 mol
Changed DataFile 'cpu-gpu-evecs.dat' type to Evecs file for set myEvecs
DIAGMATRIX: Diagonalizing matrix cpu-gpu-covar and writing modes to
cpu-gpu-evecs.dat
Calculating 3 eigenvectors.
Writing 3 modes to NMWiz file dna.nmd Storing modes with name:
myEvecs
Eigenmode calculation for 'cpu-gpu-covar'
Warning: In matrix 'cpu-gpu-covar', # of frames 534 is less than # of
columns 6117.
Warning: The max # of non-zero eigenvalues will be 534
Calculating eigenvectors and eigenvalues.
Calculating first 3 eigenmodes.
TIME: Total analysis execution time: 2.3395 seconds.
[crdaction proteina-trajectories projection CPU modes myEvecs beg 1 end 3
:1-262&!.H= crdframes 1,534]
Using set 'proteina-trajectories'
----- proteina-trajectories (1-534, 1) -----
PROJECTION: Calculating projection using eigenvectors 1 to 3 of myEvecs
Start: 1 Stop: Final frame
Atom Mask: [:1-262&!.H*]
Mask [:1-262&!.H*] corresponds to 2039 atoms.
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
TIME: Total action execution time: 0.0168 seconds.
[hist CPU:1 bins 100 out cpu-gpu-hist.agr norm name CPU-1]
Hist: cpu-gpu-hist.agr: Set up for 1 dimensions using the following
datasets:
[ Mode1 ]
norm: Sum over bins will be normalized to 1.0.
[hist CPU:2 bins 100 out cpu-gpu-hist.agr norm name CPU-2]
Hist: cpu-gpu-hist.agr: Set up for 1 dimensions using the following
datasets:
[ Mode2 ]
norm: Sum over bins will be normalized to 1.0.
[hist CPU:3 bins 100 out cpu-gpu-hist.agr norm name CPU-3]
Hist: cpu-gpu-hist.agr: Set up for 1 dimensions using the following
datasets:
[ Mode3 ]
norm: Sum over bins will be normalized to 1.0.
[hist GPU:1 bins 100 out cpu-gpu-hist.agr norm name GPU-1]
Warning: Data set 'GPU:1' not found.
Error: Dataset GPU:1 not found.
Error: Could not setup analysis [hist]
1 errors encountered reading input.
TIME: Total execution time: 15.3043 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
2017-07-03 10:36 GMT-03:00 Daniel Roe <daniel.r.roe.gmail.com>:
> 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
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Mon Jul 03 2017 - 10:00:02 PDT
