In each case you are using different trajectories and different arguments
for the rms command. Why would you expect the output to match?
-Dan
On Wed, Oct 10, 2018 at 2:16 AM DHEERAJ CHITARA <rs138.iiita.ac.in> wrote:
> Dear AMBER Users,
>
> I wish to calculate RMSD using average frame as a reference. I used the
> following input to calculate RMSD.
>
> *Input A**.*
>
> *trajin xyz.crd *
>
> *strip :Cl-,WAT*
>
> *rms first :1-801*
>
> *average crdset Ref_Ca_Avg*
>
> *run*
>
> *rms ToAvg reference :1-801.CA out Ca_Avg.dat*
> *run*
>
> *Input B**.*
> *parm topology.top *
> *loadcrd mdcrd.nc <http://mdcrd.nc/> *
>
> *crdaction mdcrd.nc <http://mdcrd.nc/> average avg.pdb .CA *
>
> *parm avg.pdb reference avg.pdb parm avg.pdb*
> *crdaction mdcrd.nc <http://mdcrd.nc/> rms reference .CA *
>
> Both input giving different different output values.
> Which is the correct way for calculating Average RMSD?
>
> Thanks in advance.
>
> --
> ----
> Dheeraj Chitara
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>
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Received on Wed Oct 10 2018 - 05:30:03 PDT
