Hm, looks like imaging artifacts to me. I'd stick an 'autoimage'
command before each 'rms' command, see if that clears things up.
-Dan
On Thu, Oct 11, 2018 at 4:23 AM DHEERAJ CHITARA <rs138.iiita.ac.in> wrote:
>
> 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
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
> --
> ----
> Dheeraj Chitara
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
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Received on Thu Oct 11 2018 - 05:30:02 PDT
