After running molecular dynamics analysis using NAMD and VMD, I uploaded the required information ( psf, coor, vel, xsc and force field files ) into the BFEE input files window to "generate the input" files for PMF, I was expecting the files with the extention ".czar.pmf" as indicated in the example but i got files with the extension ".conf and .in" what is the next step to take. i want to run MMPBSA free energy calculation from my MD simulation results
Gideon Gyebi , You will actually have to submit the configuration files generated (i.e., *.conf) in order to get the results of the calculations (which will be located in your output folder). In other words, the files you are asking about can only be obtained after running the simulations.
MMPBSA is for relative binding free energy calculations. BFEE is used to calculate absolute binding free energies. MMPBSA calculation cannot be done using the BFEE plugin. However, If you intend to calculate the absolute binding free energies, you need to do long simulations as Ernest Awoonor-Williams said.
Best,
Aziz
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