AMBER Archive (2002)

Subject: Re: Conterions

From: David Case (case_at_scripps.edu)
Date: Sat Nov 16 2002 - 13:45:01 CST

On Sat, Nov 16, 2002, Monica wrote:
>
> 1) While doing DNA-drug minimization using NMR restraints in vacuum in
> presence of conterions ,the sodium ions are forming triangulated structure
> with Phosphate of DNA.

I don't think it's generally recommended any more to do a vacuum simulation
of DNA with counterions (even with the "big" counterions that I assume you
are using). I'd recommend the GB models (with no explicit counterions)
instead, or explicit solvent calculations. But others may have more
relevant experience or answers.

> 2) Secondly I don't want to put group input on DNA while doing
> minimization but removal of group input leads planer rings of DNA -drug
> to be distorted.
>

I can't tell what sort of "group input" you have in mind, no can I tell
how non-planar the bases or drug are. More specific informations is needed.

...dac 

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