AMBER Archive (2007)

Subject: AMBER: How can i calculate generalized order parameters using ptraj.

From: cgji (cgji_at_itcc.nju.edu.cn)
Date: Sun Oct 28 2007 - 08:59:37 CST

Dear amber users ,

I want to calculate generalized order parameters of each amino acid residues (N-H vector) by molecular dynamics simulation.
And compare it to order parameters derived from NMR experiment .

It seems that ptraj support two methods suitable for calculating order parameters from dynamic trajectory .
One method calculate it directly from Legendre polynomial .
 Ane the other one calculate it using iRED technique .

>From the amber9 manual , I know some key words related to such analysis. (VECTOR , MATRIX ,ANALYZE MATRIX)

However , i don't know how to carry out such analysis exactly.

Could you please give me a copy of input file used for analyzing order parameters ?

Thank you very much for your kindly help.

2007-10-28

cgji

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