On Wed, Mar 30, 2022, Aravind R wrote:
>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).
This seems a situation where one must to MMPBSA calculations "by hand".
When breaking a covalent bond, the chemistry of the two fragments also
changes; for example, there may be extra hydrogens or capping groups that
take the place of the inter-protein bond that is being broken.
Try this: prepare three prmtop/inpcrd files, for CP, RP and LP. Then run
MMPBSA in the "stability" mode (Note 2 in Section 36.3.4) where
you just analyze a single trajectory for a single system. Do this for
each of your three systems, then combine the reults.
[The fact that the number of atoms in CP is not the sum of RP + LP will
lead to some formal errors in comparing estimated free energies. But the
ideas and insights you are looking to get from approximate methods like
MMPBSA should still be valid.]
....good luck....dac
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Received on Wed Mar 30 2022 - 06:00:04 PDT
