Hi,
It sounds like what you might want is a no-fit 2d rms plot of each residue
after fitting on a common reference frame, which could be your starting
structure, an averaged structure, etc. in cpptraj you would accomplish this
with something like:
parm myparm.parm7
reference myref.ref7
trajin traj1.nc
trajin traj2.nc
rms reference <overall fit mask>
rms2d :1 nofit out res1.gnu
rms2d :2 nofit out res2.gnu
...
And so on for each residue of interest. For each residue you will get a 2d
rms plot with 4 quadrants, where the bottom left quadrant is how the
residue moves in traj1.nc, the top right is how it moves in traj 2, and the
remaining quadrants compare how it moves between both trajectories.
Hopefully this is close to what you want,
-Dan
On Friday, February 12, 2016, Karolina Markowska <markowska.kar.gmail.com>
wrote:
> 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
> <javascript:;>>:
>
> > Karolyn's
> > My colleague Mihaly Mezei implemented a 2D rmsd comparison of two
> > trajectories.
> > Please contact him. Mihaly.mezei.mssm.edu <javascript:;>
> >
> > 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 <javascript:;>>
> > 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
> <javascript:;>>:
> > >
> > >> 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
> > >>> _______________________________________________
> > >>> AMBER mailing list
> > >>> AMBER.ambermd.org <javascript:;>
> > >>>
> >
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> > >>
> > >>
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--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Fri Feb 12 2016 - 03:00:04 PST
