[AMBER] Regarding calculation of RMSD

From: DHEERAJ CHITARA <rs138.iiita.ac.in>
Date: Mon, 1 Oct 2018 18:08:49 +0530

Dear AMBER Users,

I wish to calculate RMSD using first frame as a reference and average
pdb/frame as a reference. I used the following input to calculate RMS.

*Input A.*
*trajin xyz.crd*

*strip :Cl-,WAT *
*rms first out C_Alpha.rmsfit .CA*
*run*

*Input **B.*

*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 **C.*
*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 *

Is it the right way for calculating Average RMSD? 

-- 
----
Dheeraj Chitara
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Received on Mon Oct 01 2018 - 06:00:05 PDT
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