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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Received on Fri Oct 16 2015 - 05:30:07 PDT
