Dear Guru's,
I'm not sure I completely understand the alanine scanning
experiment/algorithm in MMPBSA.py and if anyone can set me straight, that
would be AWESOME.
Here is what I THOUGHT i needed to do.
1. create a system of 2 proteins. save prmtop and inpcrd for unsolvated
complex and individual proteins.
- solvate, minimize, heat, density, equilibrate, and then do a production
run to get snapshots. (MMPBSA calculations can be done on this alone
obviously)
2. mutate 1 residue from one protein. save prmtop and inpcrd for
unsolvated complex and individual proteins.
- solvate, minimize, heat, density, equilibrate, and then do a production
run to get snapshots. (MMPBSA calculations can be done on the mutant alone
obviously)
3. Run MMPBSA using both sets of MD snapshots to find the difference
between the 2.
in re-reading I am getting the impression that I didn't really need to do
step 2. Is that correct?
Sorry if this is basic - I think i have just confused myself...
Can I compare the energy between the 2 different MD runs directly? or
would I be missing something if I did?
Thanks,
JOnathan
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Received on Mon Dec 17 2012 - 14:30:03 PST
