I want to simulate dna intercalation. For the simulation to be correct, I need to set the pH.
I searched in the web and found that gromacs does not allow you to explicitly set pH as a modeling parameter. Instead, we protonate the protein amino acids to the pH of interest by gmx pdb2gmx.
But this is not suitable in my case, since I am researching dna. gmx pdb2gmx simply won’t be able to change charge.
So what do you recommend to do? How to set physiological pH value for simulation?
Are there methods for this in gromacs? Or similar is performed on a third-party server?
DNA force fields are by default protonated at neutral pH. Some force fields may also handle alternate tautomers, modified bases, and perhaps some protonated bases, but out of the box, you don’t need to do anything special to simulate DNA at neutral pH (assuming this is what you mean by “physiological pH”).
How to prepare any protein at physiological pH? using pdb2gmx
by default, protein is prepared at which pH using pdb2gmx?
pdb2gmx assigns protonation states at pH 7, assuming canonical pKa values for all residues in the system. For canonical DNA, nothing should be unusually protonated under these circumstances (nor would they typically be supported by any conventional force field).
Thank you for clarifying my doubt.