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 - 21:30:03 PDT
