AMBER Archive (2004)

Subject: Re: AMBER: adding ions to nucleic acids

From: Bill Ross (ross_at_cgl.ucsf.edu)
Date: Sun Feb 08 2004 - 13:40:50 CST

> i would like to minimize some nucleic acid structure
> (together w/ a protein). the na structure is of course highly
> charged and will "explode" upon minimization.

It will not explode unless there are bad vdw contacts or bad
bonds, etc. Minimization is not such a big deal, typically
just resolving slightly-bad vdw overlaps etc. Also it usually
takes but a few minutes at most, so it is better to jump in
and try it to get experience than to think about it at length
(unless it does explode).

> i order to stabilize it , i'd like to add counter ions in
> some "smart" procedure.

It is good to add ions to neutralize in any case - see advice
already sent for a way to do it. In vacuum, the 'IB' cation
may be more appropriate - this has a large size to simulate
the presence of the 1st solvation shell around a Na+ or K+ ion.

However if your goal is to use an explicit water bath, and you
think your structure is good, better to solvate, add Na+ or K+
ions as described, and follow one of the equilibration protocols
described in the equilibration FAQ.

> (i'm afraid that the ions will "over-stabilize" wrong structures
> by creating m any local energy minima).

Minimization is not a significant enough process to worry about
in this way. If the model has no major steric or bond problems,
movement will be minimal whatever you do.

Bill

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