Did you try using autoimage in the cpptraj script?
On Tue, Apr 9, 2024, 2:01 AM Priyasha Majee via AMBER <amber.ambermd.org>
wrote:
>
>
> 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 - 03:00:02 PDT
