AMBER Archive (2005)

Subject: AMBER: ptraj problem

From: Mayumi Haga (haga_at_cir.tohoku.ac.jp)
Date: Tue Feb 22 2005 - 03:38:43 CST

Dear Amber Users,

I used ptraj to know the rms value of protein in the tutorial
http://amber.scripps.edu/tutorial/plastocyanin/pcy-tutorial.html

The pdb file includes 1443 protein atoms and waters and Na+.
I wanted to know about protein's rms value, so I tried to remove waters and
Na+.

I tried two ptraj input file. I thought they would select same atoms, but
the result of out file was not same.

one input file is
*************************************************************
trajin md2.mdcrd
rms first out protein_change_first2.rms time 10
strip :WAT
strip :Na+
*************************************************************

and another input file is
******************************************************************
trajin md2.mdcrd
rms first out protein_change_first3.rms :1-1443 time 10
******************************************************************

There are not so big difference between two rms value.
I would like to know whether it's a bug or the failure of selecting atoms.

Are these two input files right for selecting atoms?

**********************************************************
Mayumi Haga
Center for Interdisciplinary Research
Tohoku University
http://rayleigh.cir.tohoku.ac.jp/
**********************************************************

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