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 Mon Apr 08 2024 - 23:30:02 PDT
