The odds of Gromacs, Nesa, Martin, . . . choosing the mutant number 5 as the best one are ten percent. Run multiple MD simulations . . . do you beat the odds by wide margin?

Hi Nesa,

I am not sure, but as far as my knowledge Gromacs only generate time dependent conformation of protein-ligand or protein-peptide complex.

you have to use other tools like GMX-PBSA, G_MMPBSA tool (rashmi kumari), or other tools to calculate binding energies of molecules on gromacs trajectory files. 

Secondly, all softwares work with particular force fields to calculate binding energy so definitely, it will vary. So, if you have to check whether the tools are giving true results or false positive results, you must use a control ligand or peptide, whose affinity is known. 

Try to generate different conformations of mutants using different force fields. And see if results match.

Regards

Tanuj Sharma

That depends - if the different mutants are very different, different programs should come more or less to the same ranking. If the differences are small, the rankings may differ, as the precision of such calculations is limited, and different forcefields may put different weights on different factors influencing the final assessment.