I have a protein-ligand (glycan) complex and want to do an MM-PBSA analysis using AMBERTOOLS after doing MDS (NAMD).
What are the files necessary I should prepare for glycan?
Note: I used CHARMM-GUI webserver to prepare the files for MDS
You can utilize cafe1.0 plugins in VMD to calculate the MM/PBSA binding energy calculation.
The link is: https://github.com/HuiLiuCode/CaFE_Plugin
Installation and User manual is inside the package.
I hope it will help.
Yes. u can calculate free energy using MM/PBSA. Please use Gromacs, VMD, and Prime for free energy calculation.
Anyone can recommend any books on such topics? Thanks in advance.
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