Hi,
Cpptraj gives results that are consistent with the DSSP program. The results are printed as fractions, not percentages like the ptraj numbers are. Multiply your cpptraj fraction by 100, and you get 97% alpha helix, which is consistent with your observation and similar to the ptraj results.
-Christina
> On Jan 17, 2016, at 6:26 AM, Sangita Kachhap <sangita.imtech.res.in> wrote:
>
>
>
> 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 - 07:00:04 PST
