GB

&gb namelist variables¶

Basic input options¶

igb (Default = 5)

Generalized Born method to use (see §4 for more info).

• 1: The Hawkins, Cramer, Truhlar pairwise GB model (GB-HCT)
• 2: Modified GB model 1 developed by A. Onufriev, D. Bashford and D.A. Case (GB-OBC1)
• 5: Modified GB model 2 developed by A. Onufriev, D. Bashford and D.A. Case (GB-OBC2)
• 7: GBn model described by Mongan, Simmerling, McCammon, Case and Onufriev (GB-Neck)
• 8: Same GB functional form as the GBn model (igb=7), but with different parameters. Developed by Nguyen, Pérez, Bermeo, and Simmerling (GB-Neck2)

alpb (Default = 0)

Use Analytical Linearized Poisson-Boltzmann (ALPB) approximation to handle electrostatic interactions within the implicit solvent model (see §4.2):

\[ ∆𝐺_{el} \approx ∆𝐺_{alpb} = -\frac{1}{2} (\frac{1}{ε_{in}} - \frac{1}{ε_{ex}})\frac{1}{1+αβ} \sum_{ij} q_{i}q_{j}(\frac{1}{f_{GB}} + \frac{αβ}{A}) \]

where \(β = \frac{ε_{in}}{ε_{ex}}\) is the ratio of the internal and external dielectrics, \(α=0.571412\), and A is the so-called effective electrostatic size of the molecule (see arad_method below). The ALPB requires one of the analytical GB models to be set, that is igb = 1, 2, 5, or 7, for computing the effective Born radii. It uses the same sets of radii as required by the particular GB model.

• 0: Don't
• 1: Use ALPB

arad_method (Default = 1)

Method used to estimate the effective electrostatic size/radius (A in ALPB equation) of the molecule (See Sigalov, Fenley, and Onufriev).

• 1: Use structural invariants
• 2: Use elementary functions
• 3: Use elliptic integral (numerical)

intdiel (Default = 1.0)

Define Internal dielectric constant.

extdiel (Default = 78.5)

Define External dielectric constant.

saltcon (Default = 0.0)

Salt concentration in Molarity (M).

rgbmax (Default = 999.0)

Distance cutoff in Å to use when computing effective GB radii.

surften (Default = 0.0072)

Surface tension value. Units in kcal/mol/Ų

surfoff (Default = 0.0)

Offset to correct (by addition) the value of the non-polar contribution to the solvation free energy term.

molsurf (Default = 0)

Define the algorithm to calculate the surface area for the non-polar solvation term.

• 0: LCPO (Linear Combination of Pairwise Overlaps)
• 1: molsurf algorithm

msoffset (Default = 0)

Offset to apply to the individual atomic radii in the system when calculating the molsurf surface. See the description of the molsurf action command in cpptraj.

probe (Default = 1.4)

Radius in Å of the probe molecule (supposed to be the size of a solvent molecule), to use when determining the molecular surface.

Note

only applicable when molsurf is set to 1

QM options¶

ifqnt (Default = 0)

Specifies whether a part of the system is treated with quantum mechanics.

• 0: Potential function is strictly classical
• 1: Use QM/MM

Keep in mind

• Calculations where part of the system is treated with quantum mechanics can be performed only with GB
• A sample QM/MMGBSA input file is shown here
• A tutorial on binding free energy calculation with QM/MMGBSA is available here

qm_theory

Which semi-empirical Hamiltonian should be used for the quantum calculation. Options are PM3, AM1, MNDO, PDDG-PM3, PM3PDDG, PDDG-MNDO, PDDGMNDO, PM3-CARB1, PM3CARB1, DFTB, SCC-DFTB, RM1, PM6, PM3-ZnB, PM3-MAIS, PM3ZNB, MNDO/D, MNDOD. The dispersion correction can be switched on for AM1 and PM6 by choosing AM1-D* and PM6-D, respectively. The dispersion and hydrogen bond correction will be applied for AM1-DH+ and PM6-DH+.

Danger

No qm_theory default, this must be specified if ifqnt = 1.

qm_residues

Complex residues to treat with quantum mechanics. All residues treated with quantum mechanics in the complex must be treated with quantum mechanics in the receptor or ligand to obtain meaningful results. This notation is the same used for print_res variable in &decomp namelist.

Danger

No qm_residues default, this must be specified if ifqnt = 1.

Selection schemes

By Distance (recommended)Amino acid selection

Notation: [ within distance ]

within corresponds to the keyword and distance to the maximum distance criterion in Å necessary to select the residues from both the receptor and the ligand. In case the cutoff used is so small that the number of qm_residues = 0, the cutoff value will be increased by 0.1 until the number of qm_residues > 0.

Example

qm_residues="within 5" Residues within 5 Å between receptor and ligand will be treated with quantum mechanic.

Notation: [ CHAIN/(RESNUM or RESNUM-RESNUM) ]

Treat with quantum mechanics residues individual or ranges. This notation also supports insertion codes, in which case you must define them individually

qm_residues="A/1,3-10,15,100" This treat with quantum mechanic Chain A residues 1, 3 through 10, 15, and 100 from the complex topology file and the corresponding residues in either the ligand and/or receptor topology files.

Let's suppose that we can have the following sequence: - A:LEU:5 - A:GLY:6:A - A:THR:6:B - A:SER:6:C - A:ASP:6:D - A:ILE:7

with the format CHAIN/RESNUMBER INSERTION_CODE

Right notationWrong notation

Ranges selection

qm_residues="A/5-7 Will treat with quantum mechanic all mentioned residues because all residues with insertion code are contained in the range

Individual selection

qm_residues="A/5,6B,6C,7 Will treat with quantum mechanic all mentioned residues except the residues 6A and 6D from chain A

Multiple chain selection

qm_residues="A/5-10,100 B/34,56 Will treat with quantum mechanic residues 5 through 10, and 100 from chain A, and residues 34 and 56 from Chain B.

qm_residues="A/5-6B,6D-7 Will end in error.

qmcut (Default = 9999.0)

The cutoff for the qm/mm charge interactions.

scfconv (Default = 1.0e-8)

Controls the convergence criteria for the SCF calculation, in kcal/mol. The tighter the convergence the longer the calculation will take. Values tighter than 1.0e-11 are not recommended as these can lead to oscillations in the SCF, due to limitations in machine precision, that can lead to convergence failures.

writepdb (Default = 1)

Write a PDB file of the selected QM region. This option is designed to act as an aid to the user to allow easy checking of what atoms were included in the QM region. Write a PDB file of the atoms in the QM region on the very first step to a file named qmmm_region.pdb.

• 0: Don't
• 1: Write a PDB file of the selected QM region

peptide_corr (Default = 0)

Apply MM correction to peptide linkages. This correction is of the form:

\[ E_{scf} = E_{scf} + h_{type}(i_{type}) * sin^{2}\phi \]

where ϕ is the dihedral angle of the H-N-C-O linkage and \(h_{type}\) is a constant dependent on the Hamiltonian used. Recommended, except for DFTB/SCC-DFTB.

• 0: Don't
• 1: Apply a MM correction to peptide linkages

verbosity (Default = 0)

Controls the verbosity of QM/MM related output. Values of 2 or higher will produce a lot of output.

• 0: only minimal information is printed - Initial QM geometry and link atom positions as well as the SCF energy at every ntpr steps.
• 1: Print SCF energy at every step to many more significant figures than usual. Also print the number of SCF cycles needed on each step.
• 2: As 1 and also print info about memory reallocations, number of pairs per QM atom, QM core - QM core energy, QM core - MM atom energy, and total energy.
• 3: As 2 and also print SCF convergence information at every step.
• 4: As 3 and also print forces on the QM atoms due to the SCF calculation and the coordinates of the link atoms at every step.
• 5: As 4 and also print all of the info in kJ/mol as well as kcal/mol.

Sample input files¶

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Sample input file for GB calculation building the Amber topologies
from structures. Please refer to the section "How gmx_MMPBSA works"

&general
startframe=5, endframe=100, interval=5, verbose=2, 
/

&gb
igb=5, saltcon=0.150,
/