it really depends on what you want to know. using the protein residues will
tell you about the changes in the overall protein structure. using the
ligand will tell you about internal changes in the ligand structure. using
both will tell you (msotly) about the protein, since it is much larger so
dominates the average. if you want to know about changes to the ligand
relative to the protein pocket (perhaps most important for a protein-ligand
complex), you can do rmsd on the protein, and then in a separate rms
command, calculate the rmsd of the ligand but without doing a best-fit to
the ligand (use "nofit" keyword at the end of that rms command). this will
align the protein to the reference structure, but then calculate the ligand
deviation while maintaining the protein alignment. The advantage of this
2-step process over just doing the rms command on the ligand without
"nofit" is that any rotatinos and translations of the ligand inside the
protein pocket will also be included in the 2-step protocol, but not
included in the 1-step protocol because you would be re-aligning on the
ligand with the 1-step protocol.
I hope that makes some sense. THe first step is to determine what you want
to learn from the rmsd data, then you can choose between the different
options. You might want to do several of these in order to learn different
things.
also note that you might need to use imaging, depending on how you set up
the initial simulations (the iwrap keyword). with iwrap=1, it is possible
that the ligand and protein might get separated in the trajectory, but that
is often just a reflection of the periodicity and not "real". doing
autoimage in cpptraj usually fixes this in your analysis. the cpptraj
manual has more information about that.
On Thu, Sep 14, 2023 at 8:29 AM VERONICA MARTIN HERNANDEZ via AMBER <
amber.ambermd.org> wrote:
> Hi everyone
>
> I have a protein-ligand complex. The protein has 305 residues and the
> ligand is the residue number 306.
>
> When I calculate the RMSD with cpptraj, what should I tell it to do,
> calculate the RMSD with the 306 total amino acids or just the ligand?
>
> I use this script:
>
> > parm 6W63-DEX.prmtop
> > trajin 6W63-DEX-NVT.nc
> > rms ToFirst :1-306 fist out rmsd1.agr mass
> > run
>
>
> Thanks in advance
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Thu Sep 14 2023 - 06:30:02 PDT
