Hi All,
I am trying to calculate the change in entropy upon protein binding. I have
performed a us scale simulations consisting of :
Just Protein A
And Protein A+ Protein B (Covalently bound).
To find the change in internal Dynamics upon protein binding, I would like
to calculate Schlitter's Entropy OR Quasi-harmonic Approach.
(like done in the following paper: Nonspecific yet decisive: Ubiquitination
can affect the native-state dynamics of the modified protein. *Protein Sci*.
2015;24(10):1580-1592. doi:10.1002/pro.2688 - Figure 10 ).
Since, in my system, the proteins are covalently bound, I get No# of atoms
in CP is not equal to RP + LP error when I use MMPBSA.py to calculate
entropy (performed as mentioned in tutorial3 section5 from amber website).
Can anyone help me understand if there is any workaround for thor OR is
there any other method to calculate Conformation entropy upon covalent
binding.
Thanks in advance!
Regards,
Aravind Ravichandran
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Received on Wed Mar 30 2022 - 04:30:02 PDT
