Re: [AMBER] RMSD of 0 for coordinated ion

From: Francesco Gentile <fgentile.ualberta.ca>
Date: Fri, 25 Mar 2016 13:23:17 -0600

Thanks Daniel, autoimage indeed works, and the RMSD appears normal now.
Thanks very much to all for your help!

--
Francesco Gentile
PhD Student, Biophysics
CCIS 3-215, Department of Physics
7-112, Li Ka Shing Centre for Health Research Innovation
University of Alberta, Edmonton, AB T6G 2E1
Canada
On 24 Mar 2016 5:19 p.m., "Francesco Gentile" <fgentile.ualberta.ca> wrote:
> Thanks very much. I realized later I was fitting to a single atom,
> obtaining consequently zero. I modified my script but I still have
> problems. basically the ion rmsd is reasonable but in some points it jumps
> to weird values such as 80+ angstroms, to return at the normal value after
> a while. I think there is something wrong in my script affecting the
> centering or something like that. My new script is
>
> trajin..
>
> image origin center familiar
>
> rms first mass out rms_back_bgw.dat ':1-132.CA,C,N' time 2.0
>
> rms first mass ':34,44' (I used this option to fit on the coordinating
> residues after the first trials but it does not change the weird behaviour)
>
> rms first mass out rms_mg_bgw.dat ':133.MG' time 2.0 nofit
> Again, the MD trajectory looks normal. Any suggestion? thanks in advance
> --
> Francesco Gentile
> PhD Student, Biophysics
> CCIS 3-215, Department of Physics
> 7-112, Li Ka Shing Centre for Health Research Innovation
> University of Alberta, Edmonton, AB T6G 2E1
> Canada
>
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Received on Fri Mar 25 2016 - 12:30:07 PDT
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