Dear all.
I want to do covariance matrix analysis using PTRAJ in Amber 9.
And Patial solvation model was used in my dynamics calculation (part of the protein was allowed to move).
So just part of the system should be included in PTRAJ ANALYSIS.
my input file ptraj.in is as follows:
[
trajin ../md2.crd
strip :WAT
matrix covar :8,13,15-24,28-60,65 82-99,105,125-143,162-237,240-259,296,314,316-329,349-371,389-410,443-450,478-491,494,497-600.CA name covar1 out covar1.dat
analyze matrix covar1 out evecs1.dat vecs 200
]
But it didn't work, for the MASK which used to select special atoms is too long .
If i reduced the MASK ,it will be ok .
how can I solve this problem ?
Many thanks. !!!!
Changge Ji
2006-11-26
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Received on Wed Nov 29 2006 - 06:07:07 PST
