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 - 01:30:03 PST
