GROMACS version:2021.1
GROMACS modification: no
Dear colleagues,
I want to perform steered molecular dynamics of a single-chain helical globular protein (apomyoglobin 153 amino acid protein) to unfold the protein. I want to apply the pulling code in one helix and other regions of the protein should be restrained. How to apply to pull force in one helix and remove retrain from that particular helix? As it is a single-chain protein I am not able to understand how to perform SMD. Looking forward for your valuable suggestions.
Thanks and regards,
Subhasree
I’m not sure if this late reply is still useful, but if you are using the pulling code following the gromacs tutorial on umbrella sampling, then you’ll see in the .mdp file provided options for specifying the pull group (Umbrella Sampling). If you need to specify a pull group that isn’t already set up, you’ll need to first make an index file specifying the atoms in each group.
Something like:
gmx make_ndx -f your_gro_file_name.gro
Options will pop up for you to specify the atoms in your new groups. Then you specify -n your_index_file_name.ndx in your gmx grompp command when you’re setting up the .tpr file to make those groups available for pulling.
Hope this helps!
Thanks a lot Karis for your valuable reply. It is indeed helpful. i just want to know when i will specify the groups for pulling rest of the part of the protein will be restrained or not. Because i have a single chain protein so it generated single posre.itp file. According to the umbrella sampling protocol in posre.itp file I have to add
#ifdef POSRES_B
#include “posre_Protein_chain_B.itp”
#endif
It was for restraining chain B. But in my care within a single chain i have to restrain the protein chain except a single helix. So how is it possible I have no idea. if you have any clue please help me to find the solution.
Thanks and regards,
Subhasreee
You can restrain any subset of atoms with an index group, as has been suggested. But I’m not sure you even need restraints here. Have you tried separating the helix without applying any restraints?
In the case of the gromacs tutorial, the reason for adding the position restraint is that they needed chain B to remain stationary in the box as a reference while chain A was moved away and allowed to unfold. If your simulation doesn’t require that, you can just remove restraints and specify the 2 pull groups as that helix and the rest of the protein, and those will be pulled away from each other. It sounds like you’re expecting to see the protein unfold by pulling on this chain, so any position restraints could stop the unfolding from happening in the restrained atoms.
If you expect to need restraints for some other reason, such as if you expect some other structure to stabilize the structure of the protein, you could remove those lines in posre_Protein_chain_B.itp corresponding to the atoms in the helix you don’t want to restrain. Looking into the .gro file (or the topol_Protein_chain_B.itp in the case that there are multiple chains) with a text editor should tell you which number corresponds to which atom.
Thank you Justin for your suggestion. No i have not tried without applying restraints. I will try this without restraint and get back to you.
Thank you so much Karis. Your suggestions have cleared my doubts. I want to see the protein unfolding with steered dynamics as apomyoglobin is very stable protein and it shows unfolding above 600k in molecular dynamics. so we thought we could apply the pulling force in the protein to see the unfolding at reasonable temperature. i was following the umbrella sampling method so I thought I should apply restraints in remaining parts of the protein. As you suggested first I will try without restraint.
I have one more doubt. Why NVT equilibration was not done in umbrella sampling protocol. Is it necessary also for me or I can do NPT followed by NPT equilibration?
I’m not sure why it was excluded from the tutorial, but in the actual paper the tutorial was based on, an NVT equilibration step is included, so I’d recommend doing so if there’s no reason not to. Also note that in the paper, 100 ns of MD simulation without restraints is run to allow the protein to relax into a conformation you’d more likely find in a real system before any pulling is done, so that’s likely best to do as well to make sure you’re starting from a realistic conformation.
We did NVT + NPT + 100 ns of MD on the original PDB structure (2BEG). A simple NPT equilibration is all that was deemed necessary when preparing the individual windows; they are already at reasonable density and arrangement of water, so the more “gentle” method of separating the two phases wasn’t really needed.
I have done NVT and NPT. Now its working fine. Thanks a lot for your guidance.