Priyasha,
just a couple of thoughts:
- Maybe the relaxation was not sufficient in the mutated system?
- Use more than a single simulation for each system to enhance your
statistics. Do you see this difference for all your simulations?
- Track down, where the high RMSD comes from: Is it the protein, the
DNA, or the complex? Maybe it's a local distortion. If on the other hand
the RMSD values of the protein and the DNA in your system remain low,
then the high RMSD comes from the relative orientation of the entities
in your system.
Maybe this helps.
Best,
Anselm
Bioinformatik | NHR.FAU
Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU)
Germany
Am 09.04.2024 um 08:00 schrieb Priyasha Majee via AMBER:
>
>
> Dear All,
>
> I am currently working with a protein-DNA complex- wild-type complex and
> single-point mutated complex. when I do the basic analysis in cpptraj, I
> find the RMSD difference to be too high. In wildtype, the RMSD with
> reference to the first frame is around 3-4 Angstroms and in mutated one
> it is around 6-10 angstrom. I was not expecting this huge change because
> the single point mutation is structurally very similar to the wildtype
> amino acid. Also, the mutated complex is obtained from the same wildtype
> structure. I tried tracking the difference. I obtained PDBs after
> minimization, heating and equilibration and superimposed the wildtype
> and mutated in PyMOL after each step. It seems after equilibration the
> structures don't superimpose. Can someone suggest me how to navigate
> through this what is going on? why the RMSD is too high despite having
> very similar structure? And how to rectify this?
>
> Thanks
>
> Regards,
>
> Priyasha
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Received on Tue Apr 09 2024 - 03:30:02 PDT
