AMBER Archive (2003)

Subject: Re: AMBER: addions/xleap question

From: Rhonda Torres (torres_at_scripps.edu)
Date: Wed Oct 01 2003 - 16:10:00 CDT

Hi Francois,

A possible reason why the Na+ ions added by the addion command do not
"follow rigouroulsy the phosphate backbone" may be due to the nature of
your model. For a "regular-backbone nucleic acids" you may indeed see
such behavior. However, if your oligo model is not regular, you should
expect to see deviations. Indeed, when I solvated a RNA-protein complex,
the Na+ ions did not rigorously follow the backbone.

Hope this helps.

Rhonda
Rhonda A. Torres
The Scripps Research Institute
Department of Molecular Biology
10550 N. Torrey Pines Rd. TPC 15
La Jolla, CA 92037

email: torres_at_scripps.edu
phone: (858) 784-9781
fax: (858) 784-8896
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