Protein in Solution: System Construction - mms-fcul/CpHMD-container GitHub Wiki
Completing the previous step, you should now have a protein structure with CpHMD compliant naming, and the required force field files (the FF folder, residuetypes.dat, and specbond.dat).
With all these files we are ready to proceed from a simple amino acid chain structure to a full system simulation box.
The first big step of a simulation setup is always to obtain a topology for our structure.
In our case, we will use the GROMACS tool pdb2gmx. The user can perform this command on their compilation of GROMACS or, if preferred, can use the GROMACS 2024.3 provided within the container without needing to install any other software!
In this tutorial we will always use the GROMACS provided within the container:
singularity exec CpHMD.sif gmx pdb2gmx -f ./<your pdb file.pdb> -p <output-name>.top -o <output-name>.gro -ignh -renum -ter
Used in the tutorial:
singularity exec CpHMD.sif gmx pdb2gmx -f ./HEWL_CpHMD.pdb -p HEWL.top -o HEWL.gro -ignh -renum -ter
The program will ask you to select the force field to be used, which should be the first option (1) since the CpHMD compatible FF is present in the folder.
Alternatively, you could provide the force field to use with the -ff command, giving the specific force field folder name, G54a7pH for GROMOS, CHARMM36pH for CHARMM36, and Amber14SBpH for AMBER.
Then you will select both the water type and the termini of your system.
Important
If your protein system has uncapped termini, you need to take note of what option to give on the termini construction. If protein termini are uncapped: When pdb2gmx asks for the termini residue you should select the option CpH+ (3) for the N-termini and CpH- (4) for the C-termini.
If the protein termini are capped: You won't need to treat these residues, hence when asked for the termini construction select None.
You are now in possession of the topology and structure.gro of your system, however it is still missing its system box and water molecules to solvate it. The steps to complete this process are as any other MD system preparation:
First you build your system box with editconf, followed by the system solvation with the solvate command:
For this tutorial:
singularity exec CpHMD.sif gmx editconf -f HEWL.gro -o HEWL_box.gro -c -d 0.9 -bt dodecahedron
singularity exec CpHMD.sif gmx solvate -cp HEWL_box.gro -cs spc216.gro -o HEWL_solv.gro -p HEWL.top
With this step, you now have your structure system complete. For a correct CpHMD usage, the next step will be the construction of the index file.
