GROMACS version:2024.4 (from conda)
GROMACS modification: Yes/No
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I tried to conduct MD simulation of protein complexes and when I did did the following error:
I disassembled the protein complex into proteins A and B in pymol
Then run the pdb2gmx，combine the gro document，add the “; Include Position restraint file”, “[ moleculetype ]”,“[ molecules ]”, in ‘top.top’
Here are my commands:
gmx pdb2gmx -f proteinA.pdb -o proteinA.gro
gmx pdb2gmx -f proteinB.pdb -o proteinB.gro
gmx editconf -f complex.gro -o complex_newbox.gro -d 1.0 -bt cubic
gmx solvate -cp complex_newbox.gro -p topol.top -o complex_solv.gro
gmx grompp -f …/…/configs/solo/ions.mdp -c complex_solv.gro -p topol.top -o complex_ions.tpr
I also found that my proteinA.itp and proteinB.itp have no 'atomtypes ’
You have constructed the topology in an incorrect order. Manual splitting of chains is unnecessary. pdb2gmx can handle multiple chains intrinsically. Let it process the dimer itself and it will write a proper topology.
Thanks for your reply,it seems work well.I also have some questions about the follow-up work: the ‘.mdp’ files used in the ions, minimization and equilibration steps are recommended in protein-ligand or in lysozyme?
Perhaps I have modified the ‘tc-grps’ in the npt.mdp and nvt.mdp of the complex, which means i need to generate ndx document.But it seems that this requires breaking the protein to do it and modifying the top file.
Now i try the follow steps to change mdp documents,and the ‘tc-grps’ = Protein Water_and_ions
commands:
gmx make_ndx -f complex.gro -o index_complex.ndx
0 & ! a H*
(This command has already generated itp by chain under pdb2gmx)
gmx genrestr -f complex.gro -n index_complex.ndx -o posre_complex.itp -fc 1000 1000 100
10
gmx make_ndx -f complex_minim.gro -o complex_minim.ndx
I choose 1|1 and 15|12，it seems no Protein_Protein generated，and Water_and_ions has already existed, which i try to generate.
You do not need to do that at all. The Protein group that may or may not be used in tc-grps is an internal GROMACS convention and the code understands all residues that constitute proteins.
Sorry, I don’t understand the question. In reality, with modern thermostats, tc-grps = System is fine. There is no longer any need to specify multiple groups.
