cgmm_model CGMM
Coarse Grained Molecular Mechanics forcefield for protein dynamics

Keep your .pdb file within folder itp_gro_file_creator.

Example: 1UBQ.pdb
 Topology file creation -
[username@hostname itp_gro_file_creator]$ perl 1UBQ
  • Output: 1UBQ.itp, and 1UBQ.gro.
  •  For metalloprotein please use metal specific code, is for Zn metal binding protein.
  •  For multimer and multidomain protein please use
  • [username@hostname itp_gro_file_creator]$ mkdir 1ubq
    [username@hostname itp_gro_file_creator]$ cp cgmm.itp 1UBQ.gro 1UBQ.itp ./1ubq

    Energy minimization step -
    [username@hostname itp_gro_file_creator]$ grompp -f ./mdp/emcg.mdp -c 1UBQ.gro -p -o 1ubq_em.tpr
    [username@hostname itp_gro_file_creator]$ mdrun -pd -v -deffnm 1ubq_em -s 1ubq_em.tpr -table ./table/table.xvg -tableb ./table/table.xvg
  • Output: Energy minimized coordinate file 1ubq_em.gro and trajectory 1ubq_em.trr

  •  Equilibrium step -
    [username@hostname itp_gro_file_creator]$ grompp -f ./mdp/eqpr.mdp -c 1ubq_em.gro -p -o 1ubq_eq.tpr
    [username@hostname itp_gro_file_creator]$ mdrun -pd -v -deffnm 1ubq_eq -s 1ubq_eq.tpr -table ./table/table.xvg -tableb ./table/table.xvg
  • Output: Equilibriate coordinate file at 298K 1ubq_eq.gro and trajectory of equilibrium 1ubq_eq.trr

  •  1 µ-second MD simulation run step -
    [username@hostname itp_gro_file_creator]$ grompp -f ./mdp/rn_1micro.mdp -c 1ubq_eq.gro -p -o 1ubq_rn.tpr
    [username@hostname itp_gro_file_creator]$ mdrun -nt 4 -pd -v -deffnm 1ubq_rn -s 1ubq_rn.tpr -table ./table/table.xvg -tableb ./table/table.xvg
  • Output: Trajectory of 1 µ-second long MD simulation 1ubq_rn.trr

  • Note:
    1. Change modified residue to normal residue in input pdb structure of, like MSE to MET (HETATM to ATOM)
    2. Use homology modelling for filling missing residues of input pdb on which you will apply