# CHARMM36 force field charge of ribonucleotide residues **URL:** \ **Category:** User discussions\ **Tags:** forcefield\ **Created:** [September 27, 2021, 2:59pm UTC](https://gromacs.bioexcel.eu/t/charmm36-force-field-charge-of-ribonucleotide-residues/2874 "2021-09-27T14:59:01Z")\ **Posts on this page:** 1\ **Showing post:** 2
**Author:** ![jalemkul](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/jalemkul/32/18_2.png) [@jalemkul](https://gromacs.bioexcel.eu/u/jalemkul)\ **Post date:** [September 28, 2021, 2:08am UTC](https://gromacs.bioexcel.eu/t/charmm36-force-field-charge-of-ribonucleotide-residues/2874/2 "2021-09-28T02:08:01Z")
> [@s.pallav](#): > > Can there be some other way round where I can read these RNA residues as neutral residues such that I don’t need to add this many number of counter-ions which influence my ligand with that high number of positive charges It makes no physical sense to do this, nor is the force field parametrized to include neutral phosphate groups in the backbone of nucleic acids. The pKa is ~2 so under all relevant biological conditions, the phosphate groups carry a -1 charge. The issue you’re probably facing is that the effective concentration of the ions is enormous for this kind of system. I’d wager that even neutralizing ions are in the high mM or near M concentration. You may want to increase the size of your box to dilute these ions to something a bit more reasonable (of course this is more expensive to simulate, but also probably more realistic). > [@s.pallav](#): > > this phenomenon happens when Particle Mesh Ewald(PME) is used to calculate long range interactions but these same ions(Na+) don’t swim near the ligand when plain cut-off is used. Plain cutoffs are entirely inaccurate and should never be used for electrostatics. Whatever you observe with a plain cutoff is fictitious. --- _[View the full topic](https://gromacs.bioexcel.eu/t/charmm36-force-field-charge-of-ribonucleotide-residues/2874)._