Hi,
you used the best fit rmsd for ion, so getting 0. value is correct. You
should add "nofit" keyword.
rms first mass out rms_back_bgw.dat ':1-132.CA,C,N' time 2.0
rms first mass out rms_mg_bgw.dat ':133.MG' time 2.0 *notfit*
You can check Jason' answer here:
http://archive.ambermd.org/201108/0809.html
(further:
https://www.google.com/webhp?sourceid=chrome-instant&ion=1&espv=2&ie=UTF-8#q=cpptraj%20nofit
)
cheers
Hai
On Thu, Mar 24, 2016 at 12:25 AM, Francesco Gentile <fgentile.ualberta.ca>
wrote:
> Hello,
> I run 100 ns of MD simulations of a protein containing a coordinated
> divalent metal ion. When calculating the RMSD, I obtain a value of 0
> angstroms for the ion, during the whole trajectory. I visualized the
> trajectory and the ion is fluctuating. here it is the script I am using for
> cpptraj
>
> trajin ...
> center :1-132 mass origin
> image origin center familiar
> rms first mass out rms_back_bgw.dat ':1-132.CA,C,N' time 2.0
> rms first mass out rms_mg_bgw.dat ':133.MG' time 2.0
>
> where residue 1-132 is the protein and 133 is the ion. I also tried to
> calculate the ion alone
>
> trajin ...
> center :133 mass origin
> image origin center familiar
> rms first mass out rms_mg_bgw.dat ':133.MG' time 2.0
>
> but still the output is 0 for all the snapshots. Could you suggest me
> possible reasons for this strange behaviour? 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 Wed Mar 23 2016 - 22:00:03 PDT
