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 Thu Mar 24 2016 - 16:30:03 PDT
