Dear all,
When I am using g_covar to calculate the covariance matrix for alpha
carbons in one subunit of my protein, I get a warning" WARNING number of
atoms in tpx (929) and trajectory (293401) do not match". 929 is the
alpha carbon number and 293401 is whole system atom number. In the
command, I used trr file and tpr file of the whole system. Do I have to
get a new trr file and tpr file just for these alpha carbons?
Some information is shown below.
"Group 0 ( System) has 293401 elements
Group 1 ( Protein) has 75295 elements
Group 2 ( Protein-H) has 38096 elements
Group 3 ( C-alpha) has 4831 elements
Group 4 ( Backbone) has 14493 elements
Group 5 ( MainChain) has 19340 elements
Group 6 (MainChain+Cb) has 23750 elements
Group 7 ( MainChain+H) has 23963 elements
Group 8 ( SideChain) has 51332 elements
Group 9 ( SideChain-H) has 18756 elements
Group 10 ( Prot-Masses) has 75295 elements
Group 11 ( Non-Protein) has 218106 elements
Group 12 ( KCX) has 184 elements
.
.
Group 107 (chO_chV_&_C-alpha) has 929 elements
Select a group: 107
Selected 107: 'chO_chV_&_C-alpha'
Calculating the average structure ...
trn version: GMX_trn_file (single precision)
Reading frame 0 time 20000.000
WARNING number of atoms in tpx (929) and trajectory (293401) do not match
Last frame 1000 time 30000.000
Last frame 1000 time 30000.000 to ./#average.pdb.17#
Read 1001 frames
Trace of the covariance matrix: 2.34563 (nm^2)
100%
Diagonalizing ...
Sum of the eigenvalues: 2.34563 (nm^2)
Writing eigenvalues to eigenval.xvg
Writing reference, average structure & eigenvectors 1--1000 to eigenvec.trr
Wrote the log to covar.log"
Tang
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