CHARMM Development Project Forums User Discussion & Questions General Chemistry Discussions nucleic acids & counter ions in minimization

i have a pdb of a nucleic acid structure that i want to minimize.
it does not contain counter ions.
how do i account for the counter ions, in order to stabilize the structure during minimization?
thanks
t.

This is a good question (but more scientific than CHARMM-specific), and I have no answer other than to look at the literature, or try to come up with a good scheme and verify that it works well.
CHARMM is a flexible research tool, and if you have an idea of to approach the scientifc problem, there is a good chance that it can be implemented easily with a CHARMM script.

Explicit water is fairly important in stabilizing nucleic acid structures, esp. DNA helical forms.

Generate the PSF for the nucleic acid; CHARMM will print the net charge. Ewald summation methods may have problems if the net charge is not zero; add enough ions to make the net charge zero.

Physical studies indicate that ions "condense" around polyanions such as DNA/RNA, so it is not unreasonable to add more ions, as long as the net charge is zero. There's some good biophysical studies on the ion distributions in the literature.