GROMACS version:2024.1
GROMACS modification: Yes/No
Hi all, I am new to using gmx_mmpbsa. May I ask if the positive energy on total column is normal for membrane protein-ligand complex, which is different from my other non-membrane protein-ligand complex systems that shows negative for total column values? Although it seems my delta energy is still negative. I have written my input parameter files here.
Input file generated by gmx_MMPBSA (1.6.4)
Be careful with the variables you modify, some can have severe consequences on the results you obtain.
General namelist variables
&general
sys_name = “Alanine_Scanning_Prot-Memb” # System name
startframe = 3501 # First frame to analyze
endframe = 9999999 # Last frame to analyze
interval = 10 # Number of frames between adjacent frames analyzed
forcefields = “oldff/leaprc.ff99SB,leaprc.gaff2” # Define the force field to build the Amber topology
ions_parameters = 1 # Define ions parameters to build the Amber topology
PBRadii = 3 # Define PBRadii to build amber topology from GROMACS files
temperature = 310.15 # Temperature
qh_entropy = 0 # Do quasi-harmonic calculation
interaction_entropy = 0 # Do Interaction Entropy calculation
ie_segment = 25 # Trajectory segment to calculate interaction entropy
c2_entropy = 0 # Do C2 Entropy calculation
assign_chainID = 0 # Assign chains ID
exp_ki = 0.0 # Experimental Ki in nM
full_traj = 0 # Print a full traj. AND the thread trajectories
gmx_path = “” # Force to use this path to get GROMACS executable
keep_files = 2 # How many files to keep after successful completion
netcdf = 0 # Use NetCDF intermediate trajectories
solvated_trajectory = 1 # Define if it is necessary to cleanup the trajectories
verbose = 1 # How many energy terms to print in the final output
/
(AMBER) Possion-Boltzmann namelist variables
&pb
ipb = 1 # Dielectric model for PB
inp = 2 # Nonpolar solvation method
sander_apbs = 0 # Use sander.APBS?
indi = 4.0 # Internal dielectric constant
exdi = 80.0 # External dielectric constant
emem = 7.0 # Membrane dielectric constant
smoothopt = 1 # Set up dielectric values for finite-difference grid edges that are located across the solute/solvent dielectric boundary
istrng = 0.150 # Ionic strength (M)
radiopt = 0 # Use optimized radii?
prbrad = 1.4 # Probe radius
iprob = 2.0 # Mobile ion probe radius (Angstroms) for ion accessible surface used to define the Stern layer
sasopt = 0 # Molecular surface in PB implict model
arcres = 0.25 # The resolution (Å) to compute solvent accessible arcs
memopt = 1 # Use PB optimization for membrane
mprob = 2.7 # Membrane probe radius in Å
mthick = 40.0 # Membrane thickness
mctrdz = 0.0 # Distance to offset membrane in Z direction
poretype = 1 # Use exclusion region for channel proteins
npbopt = 0 # Use NonLinear PB solver?
solvopt = 2 # Select iterative solver
accept = 0.001 # Sets the iteration convergence criterion (relative to the initial residue)
linit = 1000 # Number of SCF iterations
fillratio = 3 # Ratio between the longest dimension of the rectangular finite-difference grid and that of the solute
scale = 2.0 # 1/scale = grid spacing for the finite difference solver (default = 1/2 Å)
nbuffer = 0.0 # Sets how far away (in grid units) the boundary of the finite difference grid is away from the solute surface
nfocus = 1 # Electrostatic focusing calculation
fscale = 8 # Set the ratio between the coarse and fine grid spacings in an electrostatic focussing calculation
npbgrid = 1 # Sets how often the finite-difference grid is regenerated
bcopt = 10 # Boundary condition option
eneopt = 1 # Compute electrostatic energy and forces
frcopt = 0 # Output for computing electrostatic forces
scalec = 0 # Option to compute reaction field energy and forces
cutfd = 7.0 # Cutoff for finite-difference interactions
cutnb = 8.0 # Cutoff for nonbonded interations
nsnba = 1 # Sets how often atom-based pairlist is generated
decompopt = 2 # Option to select different decomposition schemes when INP = 2
use_rmin = 1 # The option to set up van der Waals radii
sprob = 0.557 # Solvent probe radius for SASA used to compute the dispersion term
vprob = 1.3 # Solvent probe radius for molecular volume (the volume enclosed by SASA)
rhow_effect = 1.129 # Effective water density used in the non-polar dispersion term calculation
use_sav = 1 # Use molecular volume (the volume enclosed by SASA) for cavity term calculation
cavity_surften = 0.0378 # Surface tension
cavity_offset = -0.5692 # Offset for nonpolar solvation calc
maxsph = 400 # Approximate number of dots to represent the maximum atomic solvent accessible surface
maxarcdot = 15000 # Number of dots used to store arc dots per atom
npbverb = 1 # Option to turn on verbose mode
/
&alanine_scanning
mutant=‘ALA’, mutant_res=‘C:398’, cas_intdiel=1
/