Simulation of Lipid Nanoparticles with PDB files curated by ATB

User discussions
1

GROMACS version: 2023.1
GROMACS modification: Yes/No

Hello,

I don’t have any previous experience in molecular dynamics, simulations, or modeling, and I feel lost in GROMACS.

The problem:

  • I use the modified forcefield provided by ATB. It is located where it should be and I always SELECT it when running “pdb2gmx”, then I keep running into the Fatal error: Residue type ‘____’ not found in residue topology database, no matter what I do.
  • I tried to modify the “residuetypes.dat” to include the unusual residues generated by ATB as Proteins, and the process runs and identifies the starting and ending termina, but then the error persists.
    I tried to modify the “topolgy.top” file to include all the generated “ITP” files by ATB, but still the error persists.

The simulation that I need to run is of a mixture of lipids (triglycerides and esters of fatty acids) and surfactant molecules. None of these molecules exist in the GROMACS database and any CHARMM or AMBER database that I could find.

I run PackMol to generate a single PDB file that incorporates all these molecules in their correct molar ratio with proper constraints, and I need to generate a topology file for this PDB, and run MD simulations.

Is this possible? or my idea is actually outside the scope of GROMACS?

2

Hello.
From the ATB server you can obtain the .itp files of the components molecules of your system and gromos54a7_atb.ff which you should extract. Combine them in your topology file like this one attached. Check the .itp files to see how the molecules are named and put it in your .top file

In the example.top file I consider LE3E, ACET and PETR as the name of the molecules and x, y and z as their number. You will how the molecules are named in the .itp file of each
example.top (414 Bytes)

Conver the pdb file you obtained from packmol to .gro and keep wprking with it together with example.top file to see.