# Adding different counter ions other than predeined in topology **URL:** \ **Category:** User discussions\ **Created:** [September 22, 2020, 5:58pm UTC](https://gromacs.bioexcel.eu/t/adding-different-counter-ions-other-than-predeined-in-topology/854 "2020-09-22T17:58:15Z")\ **Posts on this page:** 10\ **Page:** 1
**Author:** ![scinikhil](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/scinikhil/32/3483_2.png) [@scinikhil](https://gromacs.bioexcel.eu/u/scinikhil)\ **Post date:** [September 22, 2020, 5:58pm UTC](https://gromacs.bioexcel.eu/t/adding-different-counter-ions-other-than-predeined-in-topology/854/1 "2020-09-22T17:58:15Z")
GROMACS version:2020 GROMACS modification: No Here post your question Dear All, I would like to set a protein in water simulation system with **Sodium phosphate** as a counter ion. I am using AMBER ff and SPC water model. If I parameterise using antechamber and adding it in ions.itp and other related locations is a correct approach? or is there any otherway around to add different type of counter ions other than predefined.? ---
**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 22, 2020, 6:28pm UTC](https://gromacs.bioexcel.eu/t/adding-different-counter-ions-other-than-predeined-in-topology/854/2 "2020-09-22T18:28:35Z")
Na+ will already be in `ions.itp` but phosphate will not be there, nor should it. That file is for monoatomic ions only. See my post on [How to add phosphate ions in the gromacs](https://gromacs.bioexcel.eu/t/how-to-add-phosphate-ions-in-the-gromacs/852/2) about this topic. ---
**Author:** ![scinikhil](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/scinikhil/32/3483_2.png) [@scinikhil](https://gromacs.bioexcel.eu/u/scinikhil)\ **Post date:** [September 22, 2020, 6:38pm UTC](https://gromacs.bioexcel.eu/t/adding-different-counter-ions-other-than-predeined-in-topology/854/3 "2020-09-22T18:38:20Z")
Thank you @jalemkul It is a 17 aa peptide folding in water, we tried to simulate it with TIP3P and SPC water with NaCl however we seeing different secondary structure than experimentally reported (where they used phosphate ). These ions will not have an effect on small peptide folding? ---
**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 22, 2020, 7:05pm UTC](https://gromacs.bioexcel.eu/t/adding-different-counter-ions-other-than-predeined-in-topology/854/4 "2020-09-22T19:05:13Z")
I suspect it’s more likely an issue with the force field itself. Which AMBER parameter set are you using? ---
**Author:** ![scinikhil](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/scinikhil/32/3483_2.png) [@scinikhil](https://gromacs.bioexcel.eu/u/scinikhil)\ **Post date:** [September 22, 2020, 7:06pm UTC](https://gromacs.bioexcel.eu/t/adding-different-counter-ions-other-than-predeined-in-topology/854/5 "2020-09-22T19:06:19Z")
Amber14SB ---
**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 22, 2020, 8:21pm UTC](https://gromacs.bioexcel.eu/t/adding-different-counter-ions-other-than-predeined-in-topology/854/6 "2020-09-22T20:21:20Z")
Do you have a control system that you know reproduces experimental observables? It could just be a case of the model not reflecting reality, the reasons for which can be subtle. ---
**Author:** ![scinikhil](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/scinikhil/32/3483_2.png) [@scinikhil](https://gromacs.bioexcel.eu/u/scinikhil)\ **Post date:** [September 22, 2020, 8:38pm UTC](https://gromacs.bioexcel.eu/t/adding-different-counter-ions-other-than-predeined-in-topology/854/7 "2020-09-22T20:38:44Z")
Well, the peptide in water is control for us, as we need to evaluate the folding in presence of graphene sheet. We thought the reason might be due the ions used in the experimental system (Na-phosphate). I have checked with AMBER14SB along with TIP3P, SPC and SPC-E water models. Do you have any suggestions/direction to tackle this? ---
**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 23, 2020, 1:33am UTC](https://gromacs.bioexcel.eu/t/adding-different-counter-ions-other-than-predeined-in-topology/854/8 "2020-09-23T01:33:49Z")
What you’re describing doesn’t qualify as the control I was suggesting. You need a known system that has a defined experimental behavior that is similar in size to your peptide of interest, essentially to know if you should expect the force field to work well for such species. With respect to the ions, do you see any specific ion-amino acid interactions that would lead you to conclude that some spurious interaction induces structural change? If not, it’s probably not worth looking at doing anything with phosphate. Be sure you know which ion parameters are being used; there are a number of AMBER-compatible ion parameter sets and they often differ widely in their behavior. ---
**Author:** ![scinikhil](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/scinikhil/32/3483_2.png) [@scinikhil](https://gromacs.bioexcel.eu/u/scinikhil)\ **Post date:** [September 24, 2020, 6:47am UTC](https://gromacs.bioexcel.eu/t/adding-different-counter-ions-other-than-predeined-in-topology/854/9 "2020-09-24T06:47:19Z")
Yes, I have added 150mM NaCl and found that some of the ions are closely interacting with the residues. The results are different from the previous simulation where only counter ions were added. ---
**Author:** ![Bratin](https://avatars.discourse-cdn.com/v4/letter/b/f07891/32.png) [@Bratin](https://gromacs.bioexcel.eu/u/Bratin)\ **Post date:** [September 27, 2020, 2:12am UTC](https://gromacs.bioexcel.eu/t/adding-different-counter-ions-other-than-predeined-in-topology/854/10 "2020-09-27T02:12:49Z")
Hi You can use gmx insert molecule…for addition of new ions…and you can use antechamber for generating the parameters of the ions… it’s AMBER force field comparable