Hi Jan-Philip,
Thanks a lot for your help.
Now I am trying to use ptraj/cpptraj to try and find the rmsd in thefollowing
manner.
I want to align and get rmsd values of subunit B w.r.t subunit A for a snapshot.
I tried the following code:
trajin ./decamer-rep-57ns.pdb.1
reference decamer-rep-57ns.pdb.1 :1-138.CA -> to define reference
rms :139-277.CA reference -> to align subunit B on A
rms :139-277.CA reference out rmsAB.dat nofit -> to calculate rmsd of B wrt A.
But this does not work for me and I get rmsd=0.
I would look forward to your suggestions.
Thanks a lot in advance.
Best Regards,
Moitrayee
> Hello,
>
> an 'rmsd' action by default first performs a structural alignment between two
selections and then measures the distance. The alignment performed is 'sticky',
it also takes effect for all subsequent commands in a (cp)ptraj run. What you
want is possible by the combination of two 'rmsd' commands, the first performing
the alignment using a certain selection of atoms, and the second one performing
only the measurement on a different selection of atoms. The latter works with
the 'nofit' argument within an 'rmsd' command which skips alignment before
> measuring. Hence, use something like this in your input file:
>
> # Align maskA in all frames to maskA in first frame.
> # (Use rmsd command for that, but don't define output)
> rmsd maskA first
>
> # Measure distance of maskB in first frame to maskB in all frames # without
performing any structural alignment. Define an output
> # data set.
> rmsd maskB first nofit out distance.dat
>
> Note that I have only tested this in cpptraj (which you also might want to
use, especially when dealing with NetCDF trajectories).
>
> Cheers,
>
> Jan-Philip
>
>
>
>
> On 08/15/2013 04:34 AM, moitrayee.mbu.iisc.ernet.in wrote:
>> Dear All,
>> I want to do the following for an oligomer.
>> I want to superimpose each snapshot on 1 subunit and calculate time dependent
RMSD in the two neighboring subunits. Is there a way I can use ptraj to do this
>> ?
>> I would eagerly look forward to your reply.
>> Thanks a lot and Best Regards,
>> Moitrayee
>
>
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Received on Wed Aug 21 2013 - 18:30:03 PDT
