AMBER Archive (2003)

Subject: AMBER: addions/xleap question

From: FyD (fyd_at_u-picardie.fr)
Date: Wed Oct 01 2003 - 15:39:47 CDT

Dear All,

I used the "addions" xleap command (from amber7) to neutralize a simple
oligonucelotide-model. I checked the position of this Na+ ions after using this
commands. I am quite surprised because they do NOT follow rigouroulsy the
phosphate backbone: I would have expected that this each Na+ would be close to
'its' phosphate... Does it mean Na+ are more or less randomly added. It seems
NOT the case if I read the description of the addions command in the amber7
documentation. Indeed, it is written that "addions adds counterions in a shell
around unit uisng a Coulombic potential on a grid".

Thanks, 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