GROMACS version: 2023.3
GROMACS modification: Yes
Hi all! I’m having some issues trying to set up a membrane simulation with PACKMOL. I want to use decanoic acid, so I’ve tried building it with VMD Molefacture, parameterizing with CGENFF, and then running with PACKMOL. Problem is when I run pdb2gmx, I continually get the error that residues are not found in the residue topology database. I believe this is due to running simulation with custom ligand, but I was wondering if anyone has advice on how to solve this problem? I’ve also tried the same approach using a decanoic acid structure build with the CHARMMGUI ligand reader and modeler, and I get the same error. Also tried running python script that would convert nomenclature (i.e. changing “DEC” to “LIG”), but it still doesn’t work. Any tips would be much appreciated so that I can get past this issue and try actually creating a waterbox with my PACKMOL generated structure. Thank you!