Dear Daniel
Based on your good suggestion, I installed ambertools14. I used 'autoimage'
command in cpptraj and my problem was solved. Now, when I mdcrd file using
VMD, all molecules (protein + ligand + water) are inside of box.
I used following commands for autoimaging:
parm comp1_sol.prmtop
trajin prod.mdcrd
autoimage
trajout autoimaged.mdcrd
I calculated rmsd during trajectory,
parm comp1_sol.prmtop
trajin autoimaged.mdcrd
rms first mass out 1.rmsd .CA,C,N
Unfortunately, rmsd plot is unusual. There is a maximum in the plot and
rmsd values are relatively high, please note the figure in the following
link :
(
https://www.dropbox.com/s/m9xkh0g4rb7oovo/rmsd.png?dl=0)
Note that rmsd plot before and after autoimaging is the same.
Trajectory includes 10 ns (2000 frames).
Is this rmsd plot normal and usual? If not, please help me to resolve this
problem.
Best wishes,
Atila
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Received on Sat Jan 24 2015 - 11:30:02 PST
