Hello,
I am having problems with the projection in PCA using cpptraj, I get the following error
CPPTRAJ: Trajectory Analysis. V14.06b
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Reading 'WT.prmtop' as Amber Topology
INPUT: Reading Input from file matrix_1
[trajin WT_1000ns.mdcrd 900 1000]
Reading 'WT_1000ns.mdcrd' as Amber NetCDF
[matrix out correlmatrix_1000ns.dat name correlmat correl .CA]
MATRIX: Calculating correlation matrix, output is by atom
Printing to file correlmatrix_1000ns.dat
Storing matrix on internal stack with name: correlmat
Start: 1 Stop: Final frame
Mask1: .CA
[diagmatrix correlmat out evecs_1000ns.dat name evecs vecs 5]
DIAGMATRIX: Diagonalizing matrix correlmat and writing modes to evecs_1000ns.dat
Calculating 5 eigenvectors
Storing modes with name: evecs
[projection P1 modes evecs out project_1000ns.dat beg 1 end 2 .CA]
Warning: 'end' 2 is greater than # modes (0); setting end to 0
Error: 'beg' 1 out of bounds.
Error: Could not initialize action [projection]
1 errors encountered reading input.
My input file for cpptraj is:
trajin WT_1000ns.mdcrd 900 1000
matrix out correlmatrix_1000ns.dat name correlmat correl .CA
diagmatrix correlmat out evecs_1000ns.dat name evecs vecs 5
projection P1 modes evecs out project_1000ns.dat beg 1 end 2 .CA
Any help will be very appreciated as I am trying all sort of combinations, but I am not able to spot the mistake.
Many thanks in advance,
Angela
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Received on Tue Aug 19 2014 - 03:00:04 PDT
