GROMACS version:gmx2020.6_GPU
GROMACS modification: Yes/No
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The protein pdb is 1tub which has three Unique Ligands GDP,GTP,TXL. Here is the position of three ligands in the pdb. They are in the end of the PDB file， as you can see in the photo. Some one told me they are small molecules that are not covalently bonded and I should just delete them all.
So I deleted them. In the simulation, I choose the force field charmm 36. Start terminus type I choose is NH3+, end terminus I choose is Coo-. But in the Energy Minimization，I found the potential is too high which is +10000. I think it’s not right to delete the unique ligands.
; minim.mdp - used as input into grompp to generate em.tpr
; Parameters describing what to do, when to stop and what to save
integrator = steep ; Algorithm (steep = steepest descent minimization)
emtol = 1000.0 ; Stop minimization when the maximum force < 1000.0 kJ/mol/nm
emstep = 0.01 ; Minimization step size
nsteps = 50000 ; Maximum number of (minimization) steps to perform
; Parameters describing how to find the neighbors of each atom and how to calculate the interactions
nstlist = 10 ; Frequency to update the neighbor list and long range forces
cutoff-scheme = Verlet ; Buffered neighbor searching
ns_type = grid ; Method to determine neighbor list (simple, grid)
coulombtype = PME ; Treatment of long range electrostatic interactions
rcoulomb = 1.2 ; Short-range electrostatic cut-off
rvdw = 1.2 ; Short-range Van der Waals cut-off
pbc = xyz ; Periodic Boundary Conditions in all 3 dimensions
Here is the original pdb file：
1tub.txt (622.8 KB)