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Alanine Scanning

&alanine_scanning namelist variables

Keep in mind

  • A default alanine scanning input file can be created as follows:

    xbfree gmx_MMPBSA --create_input ala                # (1)!
    1. Remember to define an energy method, for example GB, PB, etc.
    xbfree amber_MMPBSA --create_input ala              # (1)!
    1. Remember to define an energy method, for example GB, PB, etc.
    xbfree namd_MMPBSA --create_input ala               # (1)!
    1. Remember to define an energy method, for example GB, PB, etc.
    xbfree charmm_MMPBSA --create_input ala             # (1)!
    1. Remember to define an energy method, for example GB, PB, etc.

  • A sample alanine scanning input file is shown here

  • A tutorial on alanine scanning is available here
mutant_res (Default = None. Must be defined)

Define the specific residue that is going to be mutated. Use the following format CHAIN/RESNUM (e.g.: A/350) or CHAIN/RESNUM INSERTION_CODE if applicable (e.g.: A/27B).

Important

  • Only one residue can be mutated per calculation!
  • For GROMACS, we recommend using the reference structure (-cr) to ensure the perfect match between the selected residue in the defined structure or topology. For AMBER, NAMD and CHARMM we recommend check carefully the structure provided (-cs).
  • When this varibale is defined, xBFreE performs the mutation. This way the user does not have to provide the mutant topology
mutant (Default = ALA)

Defines the residue that it is going to be mutated for. Allowed values are:

  • ALA or A: Alanine scanning
  • GLY or G: Glycine scanning
mutant_only (Default = 0)

Option to perform specified calculations only for the mutants.

  • 0: Perform calcultion on mutant and original
  • 1: Perform calcultion on mutant only

Note

Note that all calculation details are controlled in the other namelists, though for alanine scanning to be performed, the namelist must be included (blank if desired)

cas_intdiel (Default = 0)

The dielectric constant (intdiel(GB)/indi(PB)) will be modified depending on the nature of the residue to be mutated.

  • 0: Don’t
  • 1: Adaptative intdiel assignation

Important

  • Works with the GB and PB calculations
  • It is ignored when intdiel(GB)/indi(PB) has been explicitly defined, that is, it is ignored if intdiel != 1.0/indi != 1.0 (default values)
  • Dielectric constant values has been assigned according to Yan et al., 2017

Warning

Careful. Activating this variable can cause considerable variations in the results, since the dielectric constant of the solute varies.

intdiel_nonpolar (Default = 1)
Define the intdiel(GB)/indi(PB) value for non-polar residues (PHE, TRP, VAL, ILE, LEU, MET, PRO, CYX, ALA, GLY, PRO)
intdiel_polar (Default = 3)
Define the intdiel(GB)/indi(PB) value for polar residues (TYR, SER, THR, CYM, CYS, HIE, HID, ASN, GLN, ASH, GLH, LYN)
intdiel_positive (Default = 5)
Define the intdiel(GB)/indi(PB) value for positive charged residues (LYS, ARG, HIP)
intdiel_negative (Default = 5)
Define the intdiel(GB)/indi(PB) value for negative charged residues (GLU, ASP)
2023-11-10 2023-11-10