Olatomide Fadare

5 Questions 2 Answers 0 Followers

Questions related from Olatomide Fadare

Docking analysis of compds from gcms shows that FFA & waxes have high binding affinity 4 protein target - can this translate to in-vitro inhibition?

If docking shows that long chain hydrocarbons have high binding affinity for a particular target protein, can this really mean that the long chain HCs will have potent inhibition in-vitro or have...

01 July 2023 228 2 View

Can a Big protein be cut into domains for protein-ligand interaction MD simulation?

If my protein is large and has many domains of which one domain has the active site that I want to study ligand interaction for with MD simulation, can I cut out the domain of interest in the...

03 April 2021 8,045 3 View

How to generate toplogy for a metalloprotein?

I want to do an MD simulation of a metalloprotein with an organic ligand using gromacs and when use gmx pdb2gmx for the metalloprotein stripped of the ligand i get the following error...

21 November 2020 2,724 1 View

Which version of gromacs can i use with g_MMPBSA program (5.1.x) to calculate Free Energy after Protein Ligand Simulation?

I am currently using gromacs 2020 for my MD simulation (Protein-Ligand) and i have g_MMPBSA 5.1.x installed. after entering the command, g_mmpbsa -f md_0_10_center.xtc -s md_0_10.tpr -n index.ndx...

06 May 2020 4,106 5 View

Why does Mac version of VMD crash when loading a 3000 frame .xtc file from gromacs md simulation?

I have VMD 1.9.4 installed on a MacBook Air that crashes whenever I am loading .xtc file from a 30 ns simulation on gromacs. The .xtc file opens on the VMD installed on a linux pc without any...

11 July 2019 4,983 3 View