hello all,
I used refcoord scaling=com in npt equilibration and now running production phase with positional restraints on calcium ions in my protein when i get this warning:
"you are using pressure coupling with absolute position restraints. This will give you artifacts. Use refcoord scaling error gromacs"
What should I do? Should I use refcoord scaling = com also in the production phase? please help.
Don't use restraints in this way. Restraining the calcium while allowing the protein to be flexible is unnatural. I understand the concern about preventing Ca2+ from drifting away, but this is not the right approach. If nonbonded interactions are insufficient to keep the Ca2+ coordinated (e.g., the force field is inadequate), then the best approaches are (1) find a better force field that does not require such artificiality or (2) use distance restraints instead.
Why can't you use distance restraints? You would define a few restraints per Ca2+, involving only residues that ligate each. This is commonly done and is straightforward.
I don't know if 53A6 is suitable for such things as I have never tried it. Recent OPLS-AA modifications (to carboxylate parameters, if memory serves) improved interactions with divalent ions significantly. You may want to look at OPLS-AA, and apply those modifications.
- Badges
- Science topic