Hello Jason,
Thanks for your prompt reply. Since my protein have quiet a lot of flexible
loop regions, all I am trying to do here is to find a better alignment
before doing RMSD calculation. Hence, I hoping that
'rms reference out RMSD.dat time 2 :
1-604.CA,N,C,O' basically doing the
alignment along whole (604 residues) backbone and calculate the total RMSD.
Then, with ' rms reference out RMSD_mainloop.dat time 2
:10-40,52-74,86-223,237-287,302-318,352-372,387-485,504-528,
546-600.CA,N,C,O
' , I am trying to align the regions other than few long loops and
calculate the total RMSD .
Afterwards, with ' rms reference out RMSD_allLoop.dat time 2
:10-20,25-30,34-40,52-61,66-74,86-125,130-139,147-152,157-165,174-175,180-186,193-199,207-211,217-223,239-244,249-255,260-265,282-286,303-307,
313-318,353-358,368-371,389-392,397-405,415-421,430-434,437-461,467-484,504-512,515-524,547-564,
568-585.CA,N,C,O
' , I am trying to align regions other than all the loop regions and
calculate the total RMSD.
Am I making sense here?
Many thanks
Anu
On Fri, Oct 16, 2015 at 1:19 PM, Jason Swails <jason.swails.gmail.com>
wrote:
> On Fri, Oct 16, 2015 at 8:02 AM, anu chandra <anu80125.gmail.com> wrote:
>
> > Dear Amber users,
> >
> > I am trying to do RMSD calculation after different fitting approach
> using
> > a single cpptarj input file. I am trying to accomplish this in the
> > following way. The cpptraj.in file contains,
> >
> >
> >
> >
> ***************************************************************************************
> > trajin ../4md.crd
> >
> > autoimage
> >
> > reference ../start.crd
> >
> >
> > rms reference out RMSD.dat time 2 :1-604.CA,N,C,O
> >
> >
> > rms reference out RMSD_mainloop.dat time 2 /
> >
>
> This slash is going the wrong way, I believe. It should be \
>
>
>
> > :10-40,52-74,86-223,237-287,302-318,352-372,387-485,504-528,546-600.CA
> > ,N,C,O
> >
> >
> > rms reference out RMSD_allLoop.dat time 2
> >
> >
> :10-20,25-30,34-40,52-61,66-74,86-125,130-139,147-152,157-165,174-175,180-186,193-199,/
> >
>
> Same here (although I'm not sure if cpptraj allows you to split a single
> argument this way, so you might need to put the whole mask on a single
> line)
>
>
>
> >
> >
> 207-211,217-223,239-244,249-255,260-265,282-286,303-307,313-318,353-358,368-371,389-392,397-405,415-421,430-434,437-461,467-484,504-512,515-524,547-564,568-585.CA
> > ,N,C,O
> >
> >
> *****************************************************************************************************************
> >
> > and I run it by 'cpptraj file.top < cpptraj.in
> >
> >
> >
> > Am I doing anything wrong here?. I have seen from the tutorials that the
> > 'rms' command modify the confidantes and effect all the subsequent
> > commands. Do I need to do these three different RMSD calculation
> > separately?
> >
>
> The argument "nofit" will prevent cpptraj from rotating and translating
> the RMSD mask so as to minimize the total RMSD, and will instead just
> calculate it from the unaltered coordinates. It wasn't clear to me exactly
> what you *wanted* to be calculated. But what your script is doing (once
> the slashes are fixed) is aligning the backbone of :1-604, computing the
> RMSD, then aligning the backbone of the next residue selection and
> computing the RMSD, then aligning the backbone of the last selection of
> atoms and computing the RMSD. So the final coordinates are aligned along
> "allLoop".
>
> If you want the RMSD of different segments
>
> aligned along the *whole* backbone, then add "nofit" to your last two RMSD
> commands. But there is nothing preventing you from doing all 3 in the same
> script.
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
> _______________________________________________
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> AMBER.ambermd.org
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>
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Received on Fri Oct 16 2015 - 06:30:03 PDT
