Thanks Christina for suggestion.
On 2016-01-17 7:59 pm, Christina Bergonzo wrote:
> 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,
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--
----------------------------------------------
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 - 07:00:05 PST
