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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Received on Tue Feb 22 2005 - 09:53:00 PST
