How to simulate the stabilizing effect of trehalose towards and enzyme?

User discussions
1

GROMACS version: 2021.2
GROMACS modification: No

Hi,

I am new to GROMACS and I ran into some problems.
So far I’ve been able to simulate the dynamics of our enzyme of interest in an aqueous solution. Now I wanted to add 1M trehalose to the system and compare how it affects the natural structure of the protein.

Could anyone guide me a little bit on how I should do this?

Thanks in advance,

Marc

2

Adding molecules to a box is simple with gmx insert-molecules. Simply compute the number of necessary molecules based on your box size and tell the program to add them randomly in the box (which is what it does by default). Then proceed with adding solvent, ions, etc.

3

Hi jalemkul,

I did manage to do this but and I checked it with pymol, but somehow when I performed the solve function it lost all the trehalose molecules, i think it might be a problem of updating the topology file. Could it be?

4

After adding the trehalose, you need to update the topology manually to include its [moleculetype] definition and the number of molecules under [molecules]. If they disappeared after solvate, that’s not the program doing it (it doesn’t delete anything except water molecules it tries to add but can’t) but it doesn’t remove anything from the topology. Make sure you’re passing the correct coordinate and topology files to solvate when you add water.