Dear amber users,
I am trying to calculate in N-H bond vector order parameter using PTRAJ.
Here is the script used for the calculation.
***********************************************************
trajin ../md5.crd
vector v1 :160.N ired :160.H
vector v2 :200.N ired :200.H
vector v3 :140.N ired :140.H
vector v4 :198.N ired :198.H
vector v5 :25.N ired :25.H
matrix ired name matired order 2
analyze matrix matired order vecs 5 out ired.vec
*************************************************************
But, the calculated order parameters shows '1' for all the vectors chosen.
Below is the eigenvector file and corresponding calculated order
parameters.
ired.vec
****************************************************************
Eigenvector file: IRED
5 5
1.00000 1.00000 1.00000 1.00000 1.00000
****
1 2.30054
-0.29535 0.42414 0.61098 0.46415 -0.37965
****
2 1.13451
0.63088 0.54941 0.02842 -0.42241 -0.34770
****
3 0.76102
0.45276 0.22742 0.23157 0.37962 0.73862
****
4 0.63028
-0.54969 0.51968 0.01505 -0.49536 0.42681
****
5 0.17366
0.08720 -0.44324 0.75633 -0.46545 0.08512
*************************************************************************
############################################
************************************
- Calculated iRed order parameters -
************************************
vector S2
----------------------
0 1.00000
1 1.00000
2 1.00000
3 1.00000
4 1.00000
##############################################
Am I doing any mistakes during the calculation?. On a similar line, I have
tried to calculate the order parameters for Calpha - Cbeta bond vector
too, which also ended up with the same result of order parameters as 1.
Below is the ptraj script for the same.
**********************************************************
trajin ../md5.crd
vector v1 :160.CA ired :160.CB
vector v2 :200.CA ired :200.CB
vector v3 :140.CA ired :140.CB
vector v4 :198.CA ired :198.CB
vector v5 :25.CA ired :25.CB
matrix ired name matired order 2
analyze matrix matired order vecs 5 out ired.vec
***********************************************************
Waiting for you valuable reply.
Thanks in advance
Regards
Anu
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Received on Fri Apr 05 2013 - 00:30:02 PDT
