AMBER Archive (2008)

Subject: Re: AMBER: rms

From: Cenk \(Jenk\) Andac (cenk_andac_at_yahoo.com)
Date: Mon May 12 2008 - 08:51:56 CDT

You may want to double check the number of atoms in your COM.X, prmtop and mdcrd files to see if they match.

regards,

jenk

--- On Mon, 5/12/08, Urszula Uciechowska <urszula.uciechowska_at_pharmazie.uni-halle.de> wrote:

> From: Urszula Uciechowska <urszula.uciechowska_at_pharmazie.uni-halle.de>
> Subject: Re: AMBER: rms
> To: amber_at_scripps.edu
> Date: Monday, May 12, 2008, 8:41 AM
> 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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> >
> > --
> >
> ----------------------------------------------------------------------------
> > Dr. Vlad Cojocaru
> >
> > EML Research gGmbH
> > Schloss-Wolfsbrunnenweg 33
> > 69118 Heidelberg
> >
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> > Fax: ++49-6221-533298
> >
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> >
> > http://projects.villa-bosch.de/mcm/people/cojocaru/
> >
> >
> ----------------------------------------------------------------------------
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