Hi,
I think what you want to do is RMS with nofit- otherwise, it'll just fit
the entire thing again based on the mask. So something like-
parm mol.parm
trajin traj.nc
#align to first frame, backbone atoms
reference :1:1-370.CA,N,C,O
rms ref out rmsd.dat :1-370.CA,C,N,O
rms ref nofit out rmsd.dat :371-540.CA,C,N,O
On Mon, May 27, 2019 at 2:35 PM Hirdesh Kumar <hirdesh.iitd.gmail.com>
wrote:
> Hi,
>
> I have simulated a dimer (A: 1-370, B: 371-540)
>
> Now, I want to study the motion of 1 monomer with respect to the second
> monomer.
>
> For the same, I want to align the dimer to the chain "A" before i calculate
> the rmsd values.
>
> How should I do that?
>
>
> parm mol.parm
> trajin traj.nc
>
> #align to first frame, backbone atoms
> reference :1:1-370.CA,N,C,O
> rms ref out rmsd.dat :1-370.CA,C,N,O
> rms ref out rmsd.dat :371-540.CA,C,N,O
>
> Am I doing anything wrong?
>
>
> Thanks,
> Hirdesh
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Received on Mon May 27 2019 - 17:30:02 PDT
