I want to perform MD Simulation of Ionic compounds in Gromacs but facing problems at various points.
One of my approaches of the work is submitting the pdb files of the cations and anions to ATB server to obtain the .itp files and Gromos 54a7.ff. I build the topology from these files.
I use packmol to pack 500 anions and cations pdb files in one box and then change them to .gro.
When I proceed to minimization with this .gro file and topolgy file, Gromacs prompt fatal error of mismatch of all the atoms in topology and .gro file.
I use charmm-gui to model the cation and anion with charmm forcefield in the topology but face the same problem.
Cgenff method as in protein-ligand complex simulation gave me broken cation_ini.pdb (since the number of atoms is correct I neglect this ) but when I proceed to combine the .gro files of the ions, like proten-ligand complex to get one structure file, they appear covalently bonded or scattered in the space which is not the correct chemistry of ionic compounds.
Ligpargen, Polypargen, Acpype, and TppMkTOP servers returns error whenever I submit either of the ions to get the topology file from them.
When I use AmberTools23, I got error at the step of packing the ions together and saving the prmtop and rst7/inpcrd files of the system.
I do appreciate your patience and guiding replies.
Umar Muhammad Yahaya try ligpargen for ligand parameterization and corrected protein can be processed using Article Gmx_qk: An Automated Protein/Protein-Ligand Complex Simulati...
You can ask always your questions in the GROMACS forum and get your answer directly from gmx experts: https://gromacs.bioexcel.eu/
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