On Mon, Jan 11, 2021, Vaibhav Dixit wrote:
>I have simulated two protein structures in which only one residue was
>mutated and thus backbone sequence is the same.
>I'm guessing it must be possible to use cpptraj to align the backbone
>coordinates frame-by-frame, and estimate rmsd to check if the mutants
>sample the same conformational space.
>
>parm prot-top
>trajin prot.nc
>reference prot.inpcrd
>trajin prot1.nc parm
The command you want is "rms", something like this:
rms reference :1-141.C,CA,N out rms.dat
The manual shows lots of keywords that can be added to the rms command, but
this should get you going.
....dac
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Jan 11 2021 - 05:30:05 PST
