Conventional MMPBSA is not suitable as the forcefield will vary in amber. I do not have access to CHARMM software in our lab. Is there any other way I could compute the strength of interaction between my protein and ligand along the trajectory apart from running 3 explicit simulations for protein, ligand and protein-ligand?
For the MM interaction energy you can use the MDenergy software:
http://www.ks.uiuc.edu/Development/MDTools/mdenergy/
For solvation energy you can use APBS. For SASA term you may have to thing using other softwares (see once gromacs modules), only you have to make sure that VdW radius are the same as charmm ff. For entropic term you may use quasi-harmonic approximation, it is not difficult to find free software or write your own.
Thank you so much for your time in answering the question sir. I will look into the links and get back to you.
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