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General

&general namelist variables

Basic input options

sys_name (Default = None)

Define the System Name. This is useful when trying to analyze several systems at the same time or calculating the correlation between the predicted and the experimental energies. If the name is not defined, one will be assigned when loading the system in gmx_MMPBSA_ana on the loading order.

Tip

The definition of the system name is entirely optional, however it can provide a better clarity during the results analysis. All files associated with this system will be saved using its name.

startframe (Default = 1)
The frame from which to begin extracting snapshots from the full, concatenated trajectory comprised of every trajectory file placed on the command-line. This is always the first frame read.
endframe (Default = 9999999)
The frame from which to stop extracting snapshots from the full, concatenated trajectory comprised of every trajectory file supplied on the command-line.
interval (Default = 1)
The offset from which to choose frames from each trajectory file. For example, an interval of 2 will pull every 2nd frame beginning at startframe and ending less than or equal to endframe.

Parameter options

temperature (Default = 298.15)
Specify the temperature (in K) used in the calculations.
PBRadii (Default = "mbondi2")

PBRadii is the parameter that defines the radius that will be assigned to each atom during the calculation of the solvation energy. You can combine multiple PBRadii for the same system!

Effect of radii on energy calculations

Depending on the method selected, this parameter will have a greater or lesser impact on the computed value. While in PB, this will only be used to compute the non-polar solvation component (ENPOLAR and EDISPER). In GB, it is used, in addition to the non-polar solvation component, to compute the effective Born radius.

For gmx_MMPBSA users!

Note that notation changes from number to string. We implemented a new function to assing radii, which allow customs radii defined by de user (for example, add Au radii to the mbondi radii) through the file path.

  • bondi

    bondi radii set
    Description
    Recommended recommended when igb = 7
    Compatibility bondi is a generic radii type, which means that the radii is assigned by atom properties for any type of molecule
    Modification you can add parameters for new atoms or modify existing ones. Please see how to do it here
    Combination since bondi is a generic type, you can combine it with specific radii set (tyl06 or yamagishi). Note you can't combine it with other generic radii or complete radii types.

  • mbondi

    mbondi radii set
    Description
    Recommended recommended when igb = 1
    Compatibility mbondi is a generic radii type, which means that the radii is assigned by atom properties for any type of molecule
    Modification you can add parameters for new atoms or modify existing ones. Please see how to do it here
    Combination since mbondi is a generic type, you can combine it with specific radii set (tyl06 or yamagishi). Note you can't combine it with other generic radii or complete radii types.

  • mbondi2

    mbondi2 radii set
    Description
    Recommended recommended when igb = 2 or igb = 5
    Compatibility mbondi2 is a generic radii type, which means that the radii is assigned by atom properties for any type of molecule
    Modification you can add parameters for new atoms or modify existing ones. Please see how to do it here
    Combination since mbondi2 is a generic type, you can combine it with specific radii set (tyl06 or yamagishi). Note you can't combine it with other generic radii or complete radii types.

  • mbondi3

    mbondi3 radii set
    Description
    Recommended recommended when igb = 8
    Compatibility mbondi3 is a generic radii type, which means that the radii is assigned by atom properties for any type of molecule
    Modification you can add parameters for new atoms or modify existing ones. Please see how to do it here
    Combination since mbondi3 is a generic type, you can combine it with specific radii set (tyl06 or yamagishi). Note you can't combine it with other generic radii or complete radii types.

  • mbondi_pb2

    mbondi_pb2 radii set
    Description
    Recommended recommended when igb = 1
    Compatibility mbondi_pb2 is a generic radii type, which means that the radii is assigned by atom properties for any type of molecule
    Modification you can add parameters for new atoms or modify existing ones. Please see how to do it here
    Combination since mbondi_pb2 is a generic type, you can combine it with specific radii set (tyl06 or yamagishi). Note you can't combine it with other generic radii or complete radii types.

    It is based on mbondi radii set and contains a new optimized set of halogen PB radii for halogenated compounds (without extra point (EP) of charge) parametrized with General Amber Force Field (GAFF):

    Values from Table 3 in §3.1 Halogen Radii Optimization Without EP:

    • Cl: 1.76
    • Br: 1.97
    • I: 2.09

    This radii set should be used with the following PBSA setup:

    Sample input file for PB calculation with halogenated compounds

&general
sys_name="PB_Halogens",
PBRadii="mbondi_pb2",
/
&pb
radiopt=0, istrng=0.150, inp=1,
/

  • mbondi_pb3

    mbondi_pb3 radii set
    Description
    Recommended recommended when igb = 1
    Compatibility mbondi_pb3 is a generic radii type, which means that the radii is assigned by atom properties for any type of molecule
    Modification you can add parameters for new atoms or modify existing ones. Please see how to do it here
    Combination since mbondi_pb3 is a generic type, you can combine it with specific radii set (tyl06 or yamagishi). Note you can't combine it with other generic radii or complete radii types.

    It is based on mbondi radii set and contains a new optimized set of halogen PB radii for halogenated compounds (without extra point (EP) of charge) parametrized with General Amber Force Field (GAFF):

    Values from Table 3 in §3.1 Halogen Radii Optimization Without EP:

    • Cl: 2.20
    • Br: 2.04
    • I: 2.19

    This radii set should be used with the following PBSA setup:

    Sample input file for PB calculation with halogenated compounds

&general
sys_name="PB_Halogens",
PBRadii="mbondi_pb3",
/
&pb
radiopt=0, istrng=0.150, inp=1,
/

  • charmm_radii

    charmm_radii radii set
    Description
    Recommended recommended for CHARMM force field only. Compatible with &pb only
    Compatibility charmm_radii is a complete radii type, which means that it contain radii for protein, nucleic acids, ligands and lipids molecules
    Modification you can add parameters for new atoms or modify existing ones. Please see how to do it here
    Combination can't be combined

    This atomic radii set for Poisson-Boltzmann calculations has been derived from average solvent electrostatic charge distribution with explicit solvent. The accuracy has been tested with free energy perturbation with explicit solvent. Most of the values were taken from a *radii.str file used in PBEQ Solver in charmm-gui.

  • tyl06

    tyl06 radii set
    Description
    Recommended recommended for protein and nucleic acids only. Recommended when inp=2
    Compatibility tyl06 is a semi-complete radii type, which means that it contain radii for protein and nucleic acids molecules
    Modification you can add parameters for new atoms or modify existing ones. Please see how to do it here
    Combination can be combined with any generic radii set, for example, mbondi, mbondi2, etc.

    The Tan, Yang & Luo radii are optimized for Amber atom types as in standard residues from the Amber database. Please see the original study on how these radii are optimized.

    For Amber users!

    Note that this radii is the same applied when radiopt=1. However, as radiopt is not available in xbfree due to possible fails if the system contains other molecules types in addition to proteins and nucleic acids, then you have to apply it manually.

  • yamagishi

    yamagishi radii set
    Description
    Recommended recommended for protein and nucleic acids only.
    Compatibility yamagishi is a semi-complete radii type, which means that it contain radii for protein and nucleic acids molecules
    Modification you can add parameters for new atoms or modify existing ones. Please see how to do it here
    Combination can be combined with any generic radii set, for example, mbondi, mbondi2, etc.

    The Yamgishi radii are optimized for Amber atom types as in standard residues from the Amber database. Please see the original study on how these radii are optimized.

  • custom

    Defining a custom radii set
    Description
    Recommended it dependents of radii set type.
    Compatibility it dependents of radii set type.
    Modification you can add parameters for new atoms or modify existing ones. Please see how to do it here
    Combination it dependents of radii set type.

    You can define a new custom radii set defining the path to the radii file (*.json) as follows: PBRadii = /home/user/wdir/custom_radii.json This allows you to define specific parameters for new atoms, change existing ones, or define your set of optimized radii. Please see "How to create a custom radio set"

Entropy options

qh_entropy (Default = 0)

It specifies whether to perform a quasi-harmonic entropy (QH) approximation with cpptraj or not.

  • 0: Don’t
  • 1: perform QH

Keep in mind

  • The number of frames used for QH analyses should be higher than 3N, N being the number of atoms in the complex
  • Check this thread for more info on QH analysis
interaction_entropy (default = 0)

It specifies whether to use the Interaction Entropy (IE) approximation.

  • 0: Don’t
  • 1: perform IE

Keep in mind

  • The Interaction Entropy can be calculated independently of the solvent model used.
  • A sample Interaction Entropy input file is shown here
  • A tutorial on the use of Interaction Entropy is available here
  • The standard deviation of the interaction energy (σIE) should always be reported when using the Interaction Entropy method.
  • The Interaction Entropy method should be avoided if σIE > ~ 3.6 kcal/mol because it is impossible to converge the exponential average.
  • It is advisable to study how the Interaction Entropy depends on N by block averaging (which also provide an estimate of the precision of the calculated entropies).
  • A sampling frequency of 10 fs, as reported in the original IE publication, seems to be 3–40 times too dense. A sampling frequency of 0.1 ps would be more appropriate.
  • The Interaction Entropy results may vary depending on the system flexibility or whether constraints were used or not in the MD simulation.

Please, check this paper for further details.

ie_segment (Default = 25)
Representative segment (in %), starting from the last frame, for the calculation of the Interaction Entropy, e.g.: ie_segment = 25 means that the last quartile of the total number of frames ((endframe-startframe)/interval) will be used to calculate the average Interaction Entropy.
c2_entropy (default = 0)

It specifies whether to use the C2 Entropy approximation.

  • 0: Don’t
  • 1: perform C2

Keep in mind

  • The C2 Entropy can be calculated independently of the solvent model used.
  • A tutorial on the use of C2 Entropy is available here
  • The standard deviation of the interaction energy (σIE) should always be reported.
  • The C2 Entropy method should be avoided if σIE > ~ 3.6 kcal/mol because it gives unrealistically large entropies.
  • It is advisable to study how the C2 Entropy depends on N by block averaging (which also provide an estimate of the precision of the calculated entropies).
  • A sampling frequency of 10 fs, seems to be 3–40 times too dense. A sampling frequency of 0.1 ps would be more appropriate.
  • The C2 Entropy results may vary depending on the system flexibility or whether constraints were used or not in the MD simulation.

Please, check this paper for further details.

Miscellaneous options

assign_chainID (Default = 0)
Defines the chains ID assignment mode. It is ignored when defining a reference structure (recommended). If assign_chainID = 1, xBFreE check if the structure has no chains ID, and it is assigned according to the structure1. If assign_chainID = 2, xBFreE assign the chains ID, exist or not, according to the structure1 (can generate inconsistencies).
exp_ki (Default = 0.0)
Specify the experimental Ki (in nM) for correlations analysis. If not defined or exp_ki = 0 then this system will be omitted in the correlation analysis
full_traj (Default = 0)

Print trajectories

  • 0: Print only thread trajectories in *.mdcrd format
  • 1: Print a full traj and the thread trajectories in *.mdcrd format
exe_path

Define a list of path to search for executables (gromacs, namd, delphi, etc.). This path takes precedence over the paths defined in the PATH variable. Please,

Keep in mind

  • Note that if this variable is not defined, the necessary executables will be searched in the PATH.
  • By defining this variable you can use other versions of the same program that are in other paths than the PATH
keep_files (Default = 1)

Defines if temporary files will be deleted or not.

  • 0: Remove all temporary files
  • 1: Keep all temporary files

Keep in mind

  • Please note that temporary files may be required for compatibility with higher versions.
  • If you remove the temporary files you won't be able to do --rewrite-output to change some aspects of the output like verbose
For gmx_MMPBSA users!

Since we have improved the workflow to be more organized, this variable is different in gmx_MMPBSA. In this case, the binary file becomes the output for the default analysis.

netcdf (Default = 0)

Specifies whether to use NetCDF trajectories internally rather than writing temporary ASCII trajectory files. For very large trajectories, this could offer significant speedups, and requires less temporary space. However, this option is incompatible with alanine scanning.

  • 0: Do NOT use temporary NetCDF trajectories
  • 1: Use temporary NetCDF trajectories
process_trajectory (Default = 1)

Define if it is necessary to generate a clean trajectory, including remove water, ions or select molecules.

  • 0: Don’t
  • 1: Generate clean trajectory
For gmx_MMPBSA users!

Replace solvated_trajecotry.

verbose (Default = 1)

Specifies how much output is printed in the output file.

  • 0: Print only difference terms
  • 1: Print all complex, receptor, ligand, and difference terms

  1. The chain ID is assigned according to two criteria: terminal amino acids and residue numbering. If both criteria or residue numbering changes are present, we assign a new chain ID. If there are terminal amino acids, but the numbering of the residue continues, we do not change the ID of the chain. ↩↩

2023-11-10 2023-11-10