AMBER Archive (2005)

Subject: RE: AMBER: Pyranose pucker parameters

From: Austin B. Yongye (ayongye_at_sunchem.chem.uga.edu)
Date: Sun Feb 27 2005 - 21:08:52 CST

hey Ross,
Thanks for the response. Here are my carnal and ptraj scripts.

>> pucker parameters. Here are the first 8 lines of my output:
>>
>> L0 1.766151e-01 2.044298e+02 6.147423e-01
>> L0 7.552242e-02 2.292476e+01 4.929596e-01
>> L0 1.711139e-02 1.042250e+02 4.844757e-01
>> L0 1.149755e-01 3.181713e+02 4.895621e-01
>> L0 1.368749e-01 1.748987e+02 5.181410e-01
>> L0 4.004229e-02 2.029962e+02 5.764018e-01
>> L0 2.309195e-02 2.468739e+02 5.393260e-01
>> L0 4.703547e-03 8.509968e+01 5.157474e-01
>>

Carnal script:
FILES_IN
PARM p1 solv_nowat.top;
STREAM s1 solv_sa.crd;

FILES_OUT
TABLE tab1 pucker_params.out;

DECLARE
PUCKER puc1 6 C2 2 C3 2 C4 2 C5 2 C6 2 O6 2;

OUTPUT
TABLE tab1 puc1;
END

Ptraj script:
trajin solv_sa.crd

pucker puck2 :2_at_C2 :2_at_C3 :2_at_C4 :2_at_C5 :2_at_C6 :2_at_O6 cremer out
180_180_pucker2_pseudorot.dat
pucker puck21 :2_at_C2 :2_at_C3 :2_at_C4 :2_at_C5 :2_at_C6 :2_at_O6 cremer amplitude out
180_180_pucker2_amplitude.dat

go

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