GROMACS version: 2018
GROMACS modification: No
I am interested in performing a DNA simulation with Cobalt Hexammine +3 ions (as per Dai et al, PRL, 2008). They used the Amber force field to model the system (common for nucleic acids) and the Amber method to generate the CoHex ion parameters. I have found a website (http://amber.manchester.ac.uk/) that has proper Amber parameters for CoHex+3, but the files are in “OFF” and “FRCMOD” formats (which I believe are Amber formats). From the tutorials by @jalemkul and other information on this forum, it seems like I should use Parmed and/or Amber to convert these files to .pdb and .itp files, but I’m honestly a little lost. Finally, I assume after I do create these files, I simply use the “gmx insert molecule” to insert ions either randomly or in specific locations.
Thanks in advance for any/all help!