[gmx-users] g_mmpbsa positive binding energy

[rajendra kumar]

Hi,

MM/PBSA method has several limitations (discussed in several publications)
and therefore, you may be getting positive energy values from these
limitations. You may get a negative binding energy after further increasing
the dielectric constant, however, interpretation of this value would be
very difficult. g_mmpbsa calculates
​​
binding Enthalpy. It can be used to compare binding of several small
ligands with same receptor protein because one may assume that entropy
change is almost similar or negligible in all complexes. In case of
​ ​
large molecules binding,
​ ​
​

​binding
comparison
​s​
​are highly unreliable ​as entropy cannot be neglected
.
​ Because of these reasons, I would not use MM/PBSA method for
protein-protein complex.​


Regards,
Rajendra