Hi Amber users,
I want to calculate RMSD value with reference to Average structure. For
this I am using the following input file.
trajin 1SI2_C.050480_050490.crd
trajin 1SI2_C.050490_050500.crd
autoimage
strip :Na+,WAT
reference AVERAGE_500_50000_C.crd [500_50000_crd]
rmsd BB :1-258 .P,O3',O5',C3',C4',C5'ref [500_50000_crd] out
avg.1SI2_C.001000_051000_siRNA_Backbone.rmsfit
rmsd BB :1-258 .N,CA,C ref [500_50000_crd] out
avg.1SI2_C.001000_051000_protein_Backbone.rmsfit
rmsd BB :1-258 .P,O3',O5',C3',C4',C5',CA,C,N ref [500_50000_crd] out
avg.1SI2_C.001000_051000_Complex_All.rmsfit
rmsd BB :1-258 .CA ref [500_50000_crd] out
avg.1SI2_C.001000_051000_Protein_Alpha.rmsfit
run
But I am not getting any result and cpptraj does not process co-ordinates
after reading the frames. Result in output file is given below:
[trajin 1SI2_C.050490_050500.crd]
[1SI2_C.050490_050500.crd] contains 10 frames.
[autoimage]
AUTOIMAGE: To box center based on center of mass, anchor is first
molecule.
[strip :Na+,WAT]
STRIP: Stripping atoms in mask [:Na+,WAT]
[reference AVERAGE_500_50000_C.crd [500_50000_crd]]
Can anybody suggest me what's wrong with my input file.
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Received on Wed Jan 27 2016 - 01:30:06 PST
