AMBER Archive (2005)

Subject: Re: AMBER: ptraj problem

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On Tue, 22 Feb 2005 18:38:43 +0900, Mayumi Haga <haga_at_cir.tohoku.ac.jp>
wrote:

> I tried to remove waters and
> Na+.
>
> one input file is
> *************************************************************
> trajin md2.mdcrd
> rms first out protein_change_first2.rms time 10
> strip :WAT
> strip :Na+
> *************************************************************

You need to remove waters and Na+ ions before doing rms fitting
*************
trajin md2.mdcrd
strip :WAT,Na+
rms first out protein_change_first2.rms time 10
*************

Hope this helps!

Best Regards!

Liu

-- 
JunJun Liu
College of Chemistry
Central China Normal University
WuHan   430079
P.R. China
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