Luis Fernando Cofas-Vargas

3 Questions 11 Answers 0 Followers

Questions related from Luis Fernando Cofas-Vargas

How to calculate the deltaG binding between ATP-Mg and a protein using the MMPBSA or MMGBSA method?

From molecular dynamics simulations, using the 14SB and AMBER16 force field, I have tried to calculate the interaction between ATP-Mg and my protein of interest with the MMPBSA and MMGBSA methods,...

07 October 2022 1,768 0 View

Is it possible to average the free energy calculation using MMPBSA in different segments of a trajectory?

I would like to calculate the free energy using MMPBSA in different segments of the trajectory. These segments correspond, mostly, to the dominant conformers. Considering that these segments...

27 August 2021 4,133 3 View

What is the best way/software to define allosteric pathways?

I am trying to explain the allosteric pathway using molecular dynamics. I have tried to do a contact, correlation and hydrogen bond analysis to determine that path (using holo and apo forms). Is...

22 June 2021 3,910 13 View