AMBER Archive (2008)

Subject: Re: AMBER: rms

From: Urszula Uciechowska (urszula.uciechowska_at_pharmazie.uni-halle.de)
Date: Mon May 12 2008 - 08:41:06 CDT


this is the script that i am using:

trajin ../PROD1.mdcrd
trajin ../PROD2.mdcrd
trajin ../PROD3.mdcrd
trajin ../PROD4.mdcrd
trajin ../PROD5.mdcrd
trajin ../PROD6.mdcrd
trajin ../PROD7.mdcrd
trajin ../PROD8.mdcrd
reference ../COM.x
rms reference :1-275 out rmsd.rec.out time 0.4
rms reference :276 out rmsd.lig.out time 0.4
rms reference :1-276 out rmsd.com.out time 0.4

Is it something wrong with it?

Best Regards,
Urszula Uciechowska

MSc.PhD Student
Medicinal Chemistry Group
University of Halle-Wittenberg

----- Original Message -----
From: Vlad Cojocaru <Vlad.Cojocaru_at_eml-r.villa-bosch.de>
Date: Monday, May 12, 2008 2:45 pm
Subject: Re: AMBER: rms
To: amber_at_scripps.edu

> Hi Urszula
>
> Could you tell us the script you are using to do that? My impression
> is
> that your mask is not correct.
>
> Best
> vlad
>
> Urszula Uciechowska wrote:
> > Dear Amber users,
> >
> > I am trying to calculate rms with ptraj, but after loading my
> trajectory files i keep
> > having
> >
> > ERROR in rms: KRMS_ reported Number of atoms less than 2
> >
> > and the program quits. What is wrong?
> > thanks a lot for any help
> >
> > Best Regards,
> > Urszula Uciechowska
> >
> > MSc.PhD Student
> > Medicinal Chemistry Group
> > University of Halle-Wittenberg
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>
> --
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