I’m setting up a GROMACS simulation (10 nm box made with PACKMOL) containing water, Zn²⁺, and succinic acid using the OPLS-AA force field. Since succinic acid is not a biomolecule, pdb2gmx shows it as UNL, and external tools like LigParGen/ATB didn’t work properly. How can I generate consistent .top and .itp files for succinic acid and Zn²⁺ under OPLS-AA? If there is a better way to set up the system or an improved workflow, any insights would be really helpful.
You may try with CHARMM GUI to generate topologies.
Access link is here https://www.charmm-gui.org/?doc=sign
Hey, generating topologies for GROMACS with OPLS-AA isn't too bad, but it takes a few steps.
For succinic acid: Head to the LigParGen server (Yale's tool for OPLS params). Input the SMILES string OC(=O)CCC(=O)O (neutral form) or adjust for deprotonated if needed (e.g., charge -2 for succinate with Zn). Pick OPLS-AA, submit, and it'll spit out the .itp and .gro files ready for GROMACS.
For Zn²⁺: Standard OPLS-AA doesn't include it anymore (it was removed from ions.itp as it's not official). You'll need to make a custom .itp file. Grab literature params—like sigma = 0.21535 nm and epsilon = 1.046 kJ/mol (from common OPLS-compatible sets for Zn2+). Then, define a simple [moleculetype] section: name it ZN, add one atom with charge +2, type ZN, and those LJ values under [atoms] and [atomtypes].
Include both in your topol.top, add #include "succinic.itp" and #include "zn.itp", and you're good to go. Check a paper like the 2005 JACS on Zn simulations for exact params if possible.
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