Proein-protein interaction procedure

User discussions
1

GROMACS version:2024.4z
GROMACS modification: No
Hello all, when I conduct protein-protein interaction after finishing gromac tutorial of protein-ligand interaction, I stuck at here. In the tutorial, it writes:The ligand introduces new dihedral parameters, which were written to “jz4.prm” by the cgenff_charmm2gmx.py script. At the TOP of topol.top, insert an #include statement to add these parameters:

; Include forcefield parameters
#include “./charmm36-jul2022.ff/forcefield.itp”

; Include ligand parameters
#include “jz4.prm”

[ moleculetype ]
; Name nrexcl
Protein_chain_A 3
However, when the other ligand is another protein (not small molecules), how could I add this parameter(since there is no proteinB.prm after I conduct both protein using the following command: “gmx pdb2gmx -f proteinA_clean.pdb -o proteinA_processed.gro -p protein.top -ter” and" gmx pdb2gmx -f proteinB_clean.pdb -o proteinB_processed.gro -p proteinB.top -ter"
Whatsmore,Another problem I encountered is that it seems wrong to add
; Include Position restraint file
#ifdef POSRES
#include “proteinA.itp”
#endif

; Include ligand topology
#include “proteinB.itp”

; Include water topology
#include “./charmm36-jul2022.ff/tip3p.itp”
under this circumstances as tutorial, what change should I conduct accordingly?
Above all, when conducting protein-protein interaction, whats the difference step from gromacs tutorial’s protein-ligand interaction when establishing complex topology file?

2

If you have multiple protein chains, just run the whole complex through pdb2gmx. The protein-ligand tutorial does not apply at all in that case.

3

thanks for replying, but how could I have the complex when I only have two seperate protein file? For example. protein_A.pdb and protein_B.pdb.

4

You need to provide them as a single PDB file to pdb2gmx. The program can handle multiple chains in a single file as long as they have different chain ID or are separated by TER cards.

5

Thanks for your help!!!