GROMACS version:2021
GROMACS modification: No
My system involves a membrane protein with a dynamic alpha helix at the N-terminal domain, which interacts with the surrounding solvent. This domain is connected to a transmembrane helix domain via a loop. These two helices are nearly parallel to each other. I’ve been attempting to manipulate the mobile helix domain, aiming to make it perpendicular to the transmembrane ™ domain.
To achieve this, I’ve been using GROMACS’ COM-pulling module with an umbrella potential, along with angle or angle-axis as the coordinate geometry. I’ve also applied position restrictions to the TM domain. Unfortunately, I haven’t been successful in repositioning the mobile helix as desired.
Here are some more detailed parameters:
pull = yes
pull_ncoords = 1
pull_ngroups = 2
pull_group1_name = carbon alpha from the first residue of the helix
pull_group2_name =carbon alpha from the last residue of the helix
pull_coord1_type = umbrella
pull_coord1_geometry = angle-axis
pull_coord1_dim = Y Y Y
pull_coord1_groups = 1 2
pull-coord1-vec = 0.0 0.0 1.0
pull_coord1_start = no
pull_coord1_rate = 0.001
pull_coord1_k = 200
or:
pull = yes
pull_ncoords = 1
pull_ngroups = 2
pull_group1_name = carbon alpha from the first residue of the helix
pull_group2_name = carbon alpha from the last residue of the helix
pull_group3_name = carbon alpha from the first residue of the tm
pull_group4_name = carbon alpha from the last residue of the tm
pull_coord1_type = umbrella
pull_coord1_geometry = angle
pull_coord1_dim = Y Y Y
pull_coord1_groups = 1 2 4 3
pull_coord1_start = no
pull_coord1_rate = 0.001
pull_coord1_k = 200
I would greatly appreciate any assistance with the parameters for this task, or if anyone knows of an alternative approach to achieve this goal.
Thank you in advance for your help and insights.