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

From: DHEERAJ CHITARA <rs138.iiita.ac.in>
Date: Thu, 11 Oct 2018 13:53:10 +0530

Dear Daniel,

I used this input to generate RMSD against average coordinates only for RNA.

*RMSD from first frame*: rms first out Cr2_RNA.rmsfit .P,O3',O5',C3',C4',C5'

*RMSD for Average frame:*
rms first .P,O3',O5',C3',C4',C5'
average crdset Avg
run
rms ref Avg .P,O3',O5',C3',C4',C5' out Cr2_RNA_Mask.dat
run

But the output is incorrect. I attached RMSD graph with this mail.
In this graph the green lines shows Average RMSD of RNA and red line shows
RMSD to first frame.

Can you help me with this? I guess there is some issue with the input files
but I am unable to fix this issue ?

Thanks in advance,


On Wed, Oct 10, 2018 at 6:14 PM Daniel Roe <daniel.r.roe.gmail.com> wrote:

> 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
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> _______________________________________________
> AMBER mailing list
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>


-- 
----
Dheeraj Chitara



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RNA_Backbone.png
(image/png attachment: RNA_Backbone.png)

Received on Thu Oct 11 2018 - 01:30:02 PDT
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