Adding different counter ions other than predeined in topology

GROMACS version:2020
GROMACS modification: No
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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.?

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 about this topic.

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?

I suspect it’s more likely an issue with the force field itself. Which AMBER parameter set are you using?


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.

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?

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.

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.

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