[gmx-users] Can I align individual domains (not the whole structure) in the RMSD?

[Mark Abraham]

Hi,

On Thu, 28 Feb 2019 at 04:00 ZHANG Cheng <272699575 at qq.com> wrote:

> Sorry, can someone help me with this question? I think this question is
> very important, though it seems to be very basic. I can see in many
> publicationis, the authors do not explicitly state how the alighment is
> done for the RMSD.
>

Then I would assume the alignment selection and the computation selection
is the whole protein. Or ask the authors :-)

------------------ Original ------------------
> From:  "ZHANG Cheng"<272699575 at qq.com>;
> Date:  Wed, Feb 27, 2019 01:09 AM
> To:  "gromacs.org_gmx-users"<gromacs.org_gmx-users at maillist.sys.kth.se>;"ZHANG
> Cheng"<272699575 at qq.com>;
>
> Subject:  Can I align individual domains (not the whole structure) in the
> RMSD?
>
>
>
> My protein Fab has VH, VL, CL, CH domains. Usually in the RMSD
> calculation, I align the whole Fab first, then use a index file to
> calculate the domain's RMSD:
> $ echo 1 19 | gmx rms -s md_0_1.tpr -f md_0_1_noPBC.xtc -o rmsd.xvg -tu ns
> -n index.ndx
> (Group 1 is the whole protein, Group 19 is one of the domains)
>
>
> Now I was told to align the domain only, and then calculate the RMSD of
> that domain:
> $ echo 19 19 | gmx rms -s md_0_1.tpr -f md_0_1_noPBC.xtc -o rmsd.xvg -tu
> ns -n index.ndx
> $ echo 20 20 | gmx rms -s md_0_1.tpr -f md_0_1_noPBC.xtc -o rmsd.xvg -tu
> ns -n index.ndx
> $ echo 21 21 | gmx rms -s md_0_1.tpr -f md_0_1_noPBC.xtc -o rmsd.xvg -tu
> ns -n index.ndx
> $ echo 22 22 | gmx rms -s md_0_1.tpr -f md_0_1_noPBC.xtc -o rmsd.xvg -tu
> ns -n index.ndx
> because we want to see if the domain itself has changed (e.g. unfolded)
> throughout the trajectories, and compare which domain deforms mostly. If
> the whole structure is aligned, then the RMSD of each domain will be
> influenced by the alignment of the whole.
>

Sure

I can understand this saying. But is this really fair to align each domain?
> Is this a common practice?
>

You've aligned on the domain that you then assess the RMSD upon. If that
domain starts to unfold, you'll see that immediately, because that RMSD
can't stay constant. If you align on another domain (or all domains) then
you can no longer assess that criterion in isolation.

Mark

Also, in most cases, the domain with more residues would have higher RMSD
> if each domain is aligned.
>
>
> Thank you!
>
>
> Cheng
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