AMBER Archive (2004)

Subject: Re: AMBER: Bad atom symbol, K+ and IB in vacuum

From: David A. Case (
Date: Wed Mar 31 2004 - 12:38:47 CST

On Tue, Mar 30, 2004, Skauge Tormod wrote:
> I'm trying to run a simulation of a RNA in vacuum. As recommended in the
> amber DNA tutorial, I want to include a larger and softer counterion
> than Na+ and have tried K+ and IB. Running sander for the heating
> process (to 300K) fails with the comment "bad atom symbol: I" or "bad
> atom symbol: K".

> The "testrun" file:
> test to see if IB and K+ works
> &cntrl
> IMIN=0, NTX=1, IREST=0, NSNB=99999,
> TIMLIM=300, IG=71277, IBELLY=0,
> IGB=1, NTB=0, GBPARM=2, GBSA=0,

You say that you want to run RNA in vacuum (which I don't think is _really_
recommended in the DNA tutorial or anywhere else), yet you set igb=1, which
requests a generalized Born simulation. GB simulations are not set up to use
counterions, as counterions are treated as a part of the solvent, not part of
the solute.

You could set igb=0 to indeed get a vacuum simulation, but I cannot in good
conscience actually recommend this. Either using an explicit water or a
generalized Born model should be much better.



================================================================== David A. Case | e-mail: Dept. of Molecular Biology, TPC15 | fax: +1-858-784-8896 The Scripps Research Institute | phone: +1-858-784-9768 10550 N. Torrey Pines Rd. | home page: La Jolla CA 92037 USA | ================================================================== ----------------------------------------------------------------------- The AMBER Mail Reflector To post, send mail to To unsubscribe, send "unsubscribe amber" to