CHARMM RADII

[Carlos Chacon]

Hi everyone,

I've conducted several 50 ns simulations to check the binding energy of ATP/ADP on different conditions. For these simulations I have used the CHARMMff, adn looking at the documentation it says that I should calculate MM/PBSA.

However I obtained strange results using MM/PBSA and using GBSA I get more sensible values (And other papers also use GBSA with the charmm forcefield). My question is if it is adequate to make GBSA with CHARMM, and if so, which radii I should use for the calculations, the same as in PB (7) or the standard for GB is adequate?

Thanks in advance,

Carlos

[marioe911116]

PB model is recommended when working with CHARMMff files. Nevertheless, the combination of PB/GB models with radii optimized for amber atom types (i.e. bondi, mbondi, mbondi2, mbondi3) and CHARMM force field hasn't been tested extensively. Check this thread for more info. Presumably, as long as you use the values for relative comparison, there shouldn't be any major issues since the errors will cancel