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Input Commands

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Justin Spiriti edited this page Jun 7, 2017 · 4 revisions

This section explains all the commands used in the input file - example-go-input.txt

  1. READ FFIELD filename - Read a force field file (Tinker format). The force field file should match the force field compiler directive used to compile the program.

    READ FFIELD data/amber99sb.prm

  2. READ DEFS filename - Read a definitions file.

    READ DEFS data/defs-amber99sb.txt

  3. INSERT SEQUENCE - Add a protein chain to the system with a sequence on subsequent lines. For proteins with standard termini, the N-terminal and C-terminal amino acids must be labeled with an extra “N” or “C” ‘in the sequence as shown above. The word “END” terminates the list of residues.

 INSERT SEQUENCE
     ASNN LEU TYR ILE GLN TRP LEU LYS ASP GLY GLY PRO SER
     SER GLY ARG PRO PRO PRO SERC
 END

  1. AAREGION subset - Define the all-atom region. subset may be none, all, or a list of residue numbers and ranges.

    AAREGION none/all/

  2. READ PDB filename- Read a PDB file.

READ PDB 1l2y.pdb
  1. SEDDD epsilon(0) epsilon(1) c tol filename - Set parameters for the electrostatic interaction.
SEDDD 2.0 8.0 0.625 0.000001 data/solvpar-seddd.txt
  1. CUTOFF distance - Set the cutoff (in Å) for van der Waals and electrostatic interactions.
CUTOFF 99.0

  1. BOXSIZE length - Enable cubic periodic boundary conditions and set the box length.

  2. GO_MODEL - Introduces section with parameters for the Go model. The following subcommands are available:

a. HARDCORE radius - Set the hard core radius (r HC above) in Å.

b. NATIVE_CUTOFF distance - Set the cutoff distance for determining native contacts in the Go model.

c. EXPONENTS m n - Set the exponents m and n in the Go model.

d. WELLDEPTH energy - Set the well depth ε of the Go model.

e. NATIVE_STATE filename - Gives a PDB file with the native state.

The section must be terminated with END. An example section is as follows:

  GO_MODEL
          HARDCORE 1.7
          NATIVE_CUTOFF 8.0
          EXPONENTS 12 10
          WELLDEPTH 3.0
          NATIVE_STATE data/er-:name;-:id;-0.pdb
  END
  1. MOVES - Introduces section describing Monte Carlo move sizes and mixture. Each subsequent line names a move type, then gives the fraction of moves of that type and the maximum size. The list is terminated by END.
  MOVES
    backbone 0.50 30.0
    sidechain 0.0 0.0
    backrub 0.5 30.0
  END
  1. TEMP temperature - Set the temperature in K.
TEMP 300.0
  1. WRITE PSF filename - Write a PSF file that can be used for visualizing the trajectory in VMD (see TRAJ command below). This PSF file should not be used for analysis or simulation in CHARMM or NAMD. Also, bonds will be missing in the coarse-grained region of the protein (except for the backbone), although atoms will still be present. This may result in a strange appearance in VMD.
WRITE PSF trpcage.psf
  1. WRITE PDB filename - Write a PDB file containing the current coordinates.

WRITE PDB trpcage.pdb

  1. INSERT LIGAND residue-name - Add a ligand with the specified residue to the system. The ligand residue must be defined in the definitions file.

INSERT LIGAND ACE

  1. SEED seed - Set the random number seed (an unsigned 64-bit inte- ger). If set to zero or omitted, a random seed will be chosen based on the time.

SEED 18446744073709551615

  1. SAVEFREQ int - Set the frequency for saving frames to the the trajec- tory.

SAVEFREQ 1000

  1. PRINTFREQ int - Set the frequency for printing energies.

PRINTFREQ 1000

  1. TRAJ filename - Set the filename for writing the trajectory (DCD file format).

TRAJ DCD dcd/trpcage-go-only-1.3.dcd

  1. SETLIGANDCOM x y z - Move the ligand so that its center of mass has the given coordinates.

  2. DOCKPREP distance angle bond_angle - Prepare for docking by centering the ligand on the all-atom region and giving it a random translation, rotation, and bond rotation.

  3. ENERGY - Compute and output the energy and its terms.

  4. ENERGY LIGAND - Compute and output the internal energy of the ligand, the interaction energy of the ligand with the rest of the protein, and their component terms.

  5. RUN steps or MC steps - Run Monte Carlo for the designated number of trial moves.

RUN 100000000

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