Its been long people are using rashmi Kumari tutorial for calculating mmpbsa. But real problem comes when we generate file using latest gromacs (in my case its gromacs 2020.3) and try to calculate mmpbsa. rashmi Kumari tutorial supports end with gromacs 5.1.x and i have tried parmed.gromacs as well but everything fails.
If someone can help me in learning how to calculat mmpbsa with files obtained from gromacs 2020. It will ne a great help.
Agree!
Search Andrew Lynn Sir on RG and write to him, lets see what he says.
Use AMBER for this calculation. The python script is simple and I think that it is the most widely used program for this end-point calculation.
Zhaoxi Sun, I have tried AMBERtool. for this, it needs prmtop files which i obtained using parmed https://github.com/ParmEd/ParmEd. but even that python script lands me some kind of Radii error.
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