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.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Wed Oct 01 2003 - 21:53:01 PDT
