On Sat, Jan 24, 2015 at 2:14 PM, Atila Petrosian <atila.petrosian.gmail.com>
wrote:
> 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?
This depends strongly on your system and how flexible it is. Visualizing
the snapshots can help you understand what has happened (which often
provides clues you can use to figure out *why* it's happened). I would
suggest aligning the trajectory (or writing an aligned trajectory with
cpptraj) to avoid seeing contributions to the RMSD from simple translations
and rotations.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Sat Jan 24 2015 - 12:30:02 PST
