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 Thu Feb 11 2016 - 01:30:06 PST
