AMBER Archive (2006)

Subject: AMBER: how can i treat with long "mask" in ptraj analysis.

From: Changge Ji (
Date: Sun Nov 26 2006 - 10:22:00 CST

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 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_at_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

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