GROMACS version: 2023.3
GROMACS modification: Yes
I am trying to perform a minimization with lignin polymers. And this note appears when I use gmx grompp.
This is my topology file:
topol.top (154.3 KB)
How did you made the topology? there is something wrong in the charge assignments
thank you for your response.
I made the topology using the pdb2gmx option.
This is probably because some of your molecules have a non-integer total charge which then can not be completely neutralized by the genion passage. I think your options here are 1) run with a net charge different from zero or 2) redistribute the charges on the molecules that have non integer charge and bring the total to an integer number that you can properly neutralize. I don’t have any experience in this, but you may want to really solve this now before running sims because having a net charge will probably give rise to artifacts, while the redistribution is not trivial. Where did you take the structure from? Do you have any reference you are following or similar cases for the same molecule in literature from where you can take hints about how to proceed?
I built my structure using the SPRIG tool (https://doi.org/10.1021/acs.biomac.3c00951) and then built the 3D structures with Lignin Builder, as described in the article above. I used the CHARMM force field parameterized for lignin (https://doi.org/10.1039/C8GC03209B).
I can’t help you directly, but if in the references they have structures like yours and they don’t have left over (non-integer) charges then I guess something went wrong during your parametrisation process. As this seems to be related to a specific parametrisation which is not strictly related to GROMACS per se, I guess your best shot is to contact the authors of the paper you are citing and double check whether you are doing everything correctly and where is the possible pitfall giving you this charge.