Maryam Mappar

5 Questions 2 Answers 0 Followers

Questions related from Maryam Mappar

Is it possible to simulate an enzyme containing mercury ligand with Gromacs?

hello If the enzyme mutant contains mercury or chloride ligands in addition to the zinc ligand, Should zinc only be considered as a metal for simulation with Gromacs? Or must ligands such as...

14 January 2022 3,753 1 View

In molecular dynamics simulation I got a error to produce nvt.tpr file?

hi command : gmx grompp -f nvt.mdp -c em.gro -p topol.top -o nvt.tpr Fatal error: Cannot find position restraint file restraint.gro (option -r). From GROMACS-2018, you need to specify the...

16 September 2021 459 3 View

In molecular dynamics simulation, if we want to study enzyme activity, should the enzyme be simulated with the substrate?

Hello In molecular dynamics simulation, if we want to study enzyme activity, should the enzyme be simulated with the substrate? If the enzyme is simulated without substrate, it is not possible...

05 July 2021 3,750 5 View

Are the following conditions true for simulating the molecular dynamics of an enzyme in the blood?

hello Are the following conditions true for simulating the molecular dynamics of an enzyme in the blood? *Aquatic environment *Ph = 7 *Body temperature thank you

05 July 2021 5,103 2 View

In Molecular Dynamics Simulation, how do I make changes to the force field according to my protein?

Hi In Molecular Dynamics Simulation, how do I make changes to the force field according to my protein? I got this error in the add-ion stage: Fatal error "./ amber99sb-ildn-HHH.ff / force...

02 March 2021 9,015 4 View