Re: [AMBER] RMSD of 0 for coordinated ion

From: Daniel Roe <daniel.r.roe.gmail.com>
Date: Thu, 24 Mar 2016 19:28:25 -0600

Try 'autoimage' instead of 'image origin center familiar'. See if that
improves behavior.

-Dan

On Thu, Mar 24, 2016 at 5:19 PM, 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
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber



-- 
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Thu Mar 24 2016 - 18:30:04 PDT
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