Hi
I am doing secondary structure analysis of a protein for residues 70-77
and I am getting following format of output file.
#esidue Para Anti 3-10 Alpha Pi Turn Bend
70 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000
71 0.0000 0.0000 0.0000 0.9786 0.0000 0.0214 0.0000
72 0.0000 0.0000 0.0000 0.9786 0.0000 0.0214 0.0000
73 0.0000 0.0000 0.0011 0.9976 0.0000 0.0013 0.0000
74 0.0000 0.0000 0.0012 0.9978 0.0000 0.0011 0.0000
75 0.0000 0.0000 0.0043 0.8872 0.0000 0.1082 0.0003
76 0.0000 0.0000 0.0036 0.8223 0.0000 0.1685 0.0056
77 0.0000 0.0000 0.0032 0.3882 0.0000 0.2412 0.0000
78 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000
Earlier by using ptraj of AMBER11, I got following format of output
file.
#ResNum 3-10-Helix alpha-helix PI-Helix parallel-Sheet antip.-Sheet Turn
70 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000
71 0.632000 87.120000 0.000000 0.000000 0.000000 11.680000
72 1.088000 87.152000 0.000000 0.000000 0.000000 11.696000
73 3.400000 92.736000 0.000000 0.000000 0.000000 3.848000
74 2.920000 93.088000 0.000000 0.000000 0.000000 3.872000
75 11.840000 51.824000 0.000000 0.000000 0.000000 36.184000
76 8.728000 51.376000 0.000000 0.000000 0.000000 38.744000
77 0.384000 29.856000 0.000000 0.000000 0.000000 18.160000
78 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000
Using ptraj of amber11 I got occupancies for ALPHA like 87.120 and
87.15, suggest these residues exist as alpha helix conformation for 87%
of total simulation time but with cpptraj of amber14, occupancies are
like .9786, .9786 though these residues exist as alpha helix throughout
the simulation.
Please suggest me how to analyze the occupancies of secondary structure
calculated by cpptraj of AMBER14.
With regards
----------------------------------------------
Sangita Kachhap
Senior Research Fellow
C/O Dr. Balvinder Singh
Bioinformatics centre
CSIR-Institute of Microbial Technology
Chandigarh, Sector-39A, INDIA
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Received on Sun Jan 17 2016 - 06:00:05 PST
