AMBER Archive (2003)

Subject: Re: AMBER: addions/xleap question

From: FyD (fyd_at_u-picardie.fr)
Date: Wed Oct 01 2003 - 16:24:38 CDT

Dear Bill,

> There are some bugs in the addions code. It is not clear whether
> without these bugs you would see each ion directly on a phosphate,
> since the algorithm places an ion then adds its contribution to
> the grid before placing the next ion. Thus it is plausible that the
> 1st ion would be placed between two phosphates and things would go
> downhill from there as far as matching ions to phosphates is
> concerned.

It is exactly what I observed for a classical oligonucleotide without protein
and without unusual nucleotide....

> The main thing, no matter what placement algorithm is used, is to
> equilibrate. Once you equilibrate ions place by phosphates (as the
> old Edit program did), you will see the ions in random-appearing
> positions, typically with some ion pairs formed with pairs of waters.

OK it makes perfect sens, now.

Thank you very much, best regards, Francois

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu