Luis Fernando Cofas-Vargas

5 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 1,819 0 View

Does anyone know why MMPBSA.py currently cannot do non-polar solvation decomposition in the MMPBSA approach?

I would like to understand why MMPBSA.py can decompose non-polar solvation energies in GBSA method, but not with PBSA, if they both have a similar approach to calculate that value.

11 May 2022 7,848 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 4,168 3 View

Has anyone done inhibition assays of FOF1-ATP synthase with aurovertin?

We are looking for experimental validation of the inhibition susceptibility of F1 sectors from different species. We have done an exhaustive literature search and are interested in data that, for...

01 July 2021 8,294 0 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 3,979 13 View