Parameterize Residues

With the exception of water, we parameterize all monomers and solutes with the general Amber force field (GAFF). To add GAFF parameters, we use the antechamber package which comes with AmberTools. See their download page to obtain the software for your machine. antechamber’s primary role is to identify GAFF atom types and assign the corresponding bond, pair, angle, dihedral and improper dihedral parameters. It also uses the AM1-BCC method in order to assign charges to the atoms.

The AM1-BCC method is flawed in that it can easily assign charges asymetrically to an otherwise symmetric molecule. We avoid this issue by re-assigning charges with am1bccsym method of molcharge, a python script shipped with QUACPAC from OpenEye Scientific.

Our general workflow for parameterizing a molecule with GAFF is:

  1. Generate an initial structure. You will have the easiest time with a reasonable approximation of the 3D structure. I recommend using a tool like MarvinSketch which is capable performing a crude energy minimization in order to arrange a molecule in 3D space.
  2. Run antechamber to assign parameters and initial charges.
  3. Energy minimize the structure using GAFF params.
  4. Re-assign charges with molcharge.
  5. Energy minimize.
  6. (optional) Run an MD simulation in order to get new conformations. Sometimes this is necessary in order to get a monomer into a configuration that can easily be built into an HII unit cell.

The above steps are written in parameterize.py

from LLC_Membranes.setup import parameterize

Command Line Interface

Parameterize a solute with a force field

usage: parameterize.py [-h] [-p PDB_FILE] [-o OUTPUT_NAME] [-m MDP_FILE]
                       [-n NET_CHARGE] [-ff FORCE_FIELD] [-f FORMAT]
                       [--tinker]

Named Arguments

-p, --pdb_file Input .pdb file
-o, --output_name
 String for names of output files.
-m, --mdp_file gromacs .mdp file for energy minimization.
-n, --net_charge
 

net charge on molecule

Default: 0

-ff, --force_field
 

Name of force field used to assignparameters.

Default: “gaff”

-f, --format

Format of output topology and coordinatefiles.

Default: “gromacs”

--tinker

Convert gromacs topolgy to Tinker .prm and determine energy differences

Default: False

Classes

class parameterize.Parameterize(pdb, output, mdp='em.gro', output_format='gromacs', net_charge=0)
__init__(pdb, output, mdp='em.gro', output_format='gromacs', net_charge=0)

Parameterize a molecule. Currently only GAFF is implemented.

Parameters:
  • pdb (str) – name of structure file in PDB format
  • output (str) – name output residue
  • mdp (str) – name of mdp file with which to perform energy minimization
  • output_format (str) – Name of program for which output topology and coordinate files should be generated
  • net_charge (int) – net charge on molecule
assign_gaff_parameters()

Call antechamber in order to assign atomtypes and charges

assign_molcharge_charges()

Use molcharge to assign charges based on a coordinate file

convert_parameter_format()

Use parmed to convert amber parameters to different format

energy_minimize(convert_to_pdb=True)

Energy minimize the

Returns:
make_box(d=3, out='box.gro')

Put a box around the solute

Parameters:
  • d (float) – minimum distance between solute and edge of box
  • out (str) – name of output boxed solute