CGMM Coarse Grained Molecular Mechanics forcefield for protein dynamics

TUTORIAL

Keep your .pdb file within folder itp_gro_file_creator.

Example: 1UBQ.pdb

Topology file creation -

[username@hostname itp_gro_file_creator]$ perl pdb2ItpGroTop.pl 1UBQ

Output: 1UBQ.itp,1UBQ.top and 1UBQ.gro.  For metalloprotein please use metal specific code, pdb2ItpGroTop_Zn.pl is for Zn metal binding protein.  For multimer and multidomain protein please use pdb2ItpGroTop_multimer_multidomain.pl

[username@hostname itp_gro_file_creator]$ mkdir 1ubq

[username@hostname itp_gro_file_creator]$ cp cgmm.itp 1UBQ.gro 1UBQ.itp 1UB.top ./1ubq

Energy minimization step -

[username@hostname itp_gro_file_creator]$ grompp -f ./mdp/emcg.mdp -c 1UBQ.gro -p 1UBQ.top -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 1UBQ.top -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 1UBQ.top -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 pdb2ItpGroTop.pl, like MSE to MET (HETATM to ATOM)

2. Use homology modelling for filling missing residues of input pdb on which you will apply pdb2ItpGroTop.pl

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