Thank you, Bill and Anselm for your advices,
I think I will try the 2D-RMSD-plot first.
Have a nice day!
Karolina
2016-02-11 10:27 GMT+01:00 Dr. Anselm Horn <anselm.horn.fau.de>:
> Dear Karolina,
>
> AFAIK a 'reference' is limited to a single structure.
>
> Reading in two trajectories in a row should be no problem for cpptraj,
> as you can give several trajin commands.
> For the comparison of the two trajectories you could then use e.g. a
> 2D-RMSD-plot or perform a cluster analysis on the combined trajectories
> with a subsequent inspection of the distribution of the cluster
> structures between the trajectories. Or you could monitor some other
> properties of interest and compare those values.
>
> Regards,
>
> Anselm
>
>
> Am 11.02.2016 10:07, schrieb Karolina Markowska:
> > Dear Amber Users,
> >
> > I have two simulations with the same system and I would like to compare
> > them. Mostly I would like to check if I'm having the same protein
> > conformations in these two simulations. Does Amber software provide a
> tool
> > for that kind of analysis?
> >
> > I wanted to use cpptraj and use the first trajectory as reference, add
> the
> > second one by trajin and calculate rmsd between them, but cpptraj uses
> only
> > the first frame from that file. Can I make cpptraj to read whole
> trajectory
> > as a reference?
> > The script looked like that:
> >
> > parm protein.prmtop
> > reference sim1.nc
> > trajin sim2.nc
> > autoimage
> > strip :WAT
> > strip :Na+
> > rms ToRef :1-340.CA,C,N= reference out rmsd.arg mass
> > quit
> >
> > | sim1.nc is the trajectory of the first simulation and sim2.nc is the
> > trajectory from the second simulation.
> >
> > Thanks for your help.
> > Best regards,
> > Karolina Markowska
> > PhD student
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> >
> >
>
>
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Received on Thu Feb 11 2016 - 02:00:03 PST
