I read thie article below.
:Comparative Molecular Field Analysis (CoMFA). 1. Effect of Shape on Binding of Steroids to Carrier Proteins
I have PDB files (also PQR) and I'd like to do CoMFA to PDB (PQR) files in command line (not GUI software).
Now I want the program calculating energies of van der waals and electrostatic interaction from PDB files (Python is best).
Especially, van der waals force has different values between the pair of atoms (C and N and C and O has different values), so it is complex and bothersome to write a program which works quickly.
In addition, as far as I searched, van der waals energy is expressed by Lennard Jones potential in many articles. I want to know what formula does generally express van der waals energy in area of 3D-QSAR?.
Thank you for reading.
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