[AMBER] Regarding calculation of RMSD using AMBER-18 CPPTRAJ V-18.01

From: DHEERAJ CHITARA <rs138.iiita.ac.in>
Date: Wed, 10 Oct 2018 11:45:50 +0530

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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Received on Tue Oct 09 2018 - 23:30:02 PDT
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