Thank you all very much for your help!
After a consultation with my boss, we decided, we're looking for something
that could provide us something like a 2D-RMSD plot, but for each amino
acid separately - so something more like 2D-RMSF :)
The 2D-RMSD plot would be OK, but we're interested in comparing the
movement of each amino acid. The question we want to answer is - does this
amino acid behave _like this_ in both simulations or just in one case?
Can you help us?
Have a nice day!
Karolina
2016-02-11 16:40 GMT+01:00 Osman, Roman <roman.osman.mssm.edu>:
> Karolyn's
> My colleague Mihaly Mezei implemented a 2D rmsd comparison of two
> trajectories.
> Please contact him. Mihaly.mezei.mssm.edu
>
> I used it and it's a great tool
>
> Roman Osman
> Sent from my iPhone
>
> > On Feb 11, 2016, at 4:45 AM, Karolina Markowska <markowska.kar.gmail.com>
> wrote:
> >
> > 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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Received on Fri Feb 12 2016 - 00:30:04 PST
