GROMACS version: 2021
GROMACS modification: No
Hi everyone,
I am trying to perform a steered MD by pulling a ligand through a beta-barrel kind of membrane protein. As a starting configuration, I have put the ligand (a small cyclic sugar) on top of one of the openings of the beta-barrel protein and intend to pull the ligand through the protein along the z-direction (axis of the beta-barrel). So the protein is like a hollow cylinder with two openings: top and bottom (like a barrel made of beta sheets). I have made two separate index groups one for ligand and one for protein respectively. I am using the following pull-code settings:
; Pull code
pull = yes
pull_ncoords = 1 ; only one reaction coordinate
pull_ngroups = 2 ; two groups defining one reaction coordinate
pull_group1_name = LIG
pull_group2_name = PROT
pull_coord1_type = umbrella ; harmonic potential
pull_coord1_geometry = distance ; simple distance increase
pull_coord1_dim = N N Y ; pull along z
pull_coord1_groups = 1 2 ; groups 1 (Chain A) and 2 (Chain B) define the reaction coordinate
pull_coord1_start = yes ; define initial COM distance > 0
pull_coord1_rate = 0.01 ; 0.01 nm per ps = 10 nm per ns
pull_coord1_k = 1000 ; kJ mol^-1 nm^-2
I am getting the following grompp error: “When the maximum distance from a pull group reference atom to other atomsin the group is larger than 0.5 times half the box size a centrally placed atom should be chosen as pbcatom. Pull group 2 is larger than that and does not have a specific atom selected as reference atom.”
I understand that this error refers to the fact that the beta-barrel protein diameter or distance from bottom to the top opening is larger than the half z-box vector. Since, this is a hollow cylinder looking protein (beta-barrel), there is no protein atom present at the center of geometry or center of mass that can be selected as pbcatom;
So my first question is: is there any other way or pull settings I can use to pull the ligand through the protein using protein-ligand distance as reaction coordinate
question-2: I have also tried to use the N-terminal C-alpha atom instead of the entire protein as a separate index group and tried to use center-center distance between N-term CA-LIG as reaction coordinate; In this case the pulling works and the ligand starts translocating through the protein; However the N-terminal part also starts to drift largely from its original positiona and once the ligand is very close to the N-term CA, the secondary structure changes (in the N-term region) from helix to coil---- which I think is not a right thing to happen;
So my second question is: is there a possibility where only the ligand will be pulled towards the protein not the N-term CA, so the secondary structure is conserved?
Thanks in advance