Subject: counterions for N.A.

From: "Don Gregory" <[email-masked]>
Date: 10 Oct 1994 09:39:53 +0000

Subject:                               Time:10:51
AM
  OFFICE MEMO          counterions for N.A.                   Date:10/9/94
To accompany Drs. Monaco and Loomis' note on their mac program for
generating ions around nucleic acids:

"	We have written a Mac application, CounterIon 1.0, which will place
counterions around a DNA helix (from a pdb file format). This may be
useful to users of CHARMm ..."

We, too, have heard this request from a number of users; note the
spirited discussion on this BBS a number of weeks ago about
empirical and theoretical investigations into the "appropriate"
number of counter ions around nucleic acids.
For working with CHARMm, I recently created a CHARMm RTF
file for DNA which places a sodium ion near the phosphate
oxygens.  As an example as to how easily this could be done,
we have provided this RTF file on our anon. ftp server
(server.msi.com: archives/quanta/dna_na.rtf.Z and 	dnaions.txt.Z)
This RTF can be used both with QUANTA/CHARMm, and with 
CHARMm standalone.
This file not meant as a reference on the positioning, nor the
number of recommended counter ions around nucleic acid, but
rather a template as to how one may include them should one
wish.
Don Gregory
Mgr.Appl.Science, MSI

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From: [email-masked] (Brian A. Kell)
Date: Mon, 10 Oct 94 16:14:47 EDT

At the risk of sounding like a "me too"...

Last December, a BCL macro for InsightII was posted on the DIBUG
(Discover and Insight -- Biosym Users' Group) mailing list, which also
places specified counterions around DNA molecules.  It is available in
the DIBUG archives.  Or, I can send it directly to interested parties.

brian

------------------------------------------------------------------
Brian Kell                                          [email-masked]
Scientific Support Manager, Eastern Region     Tel. (518) 482-1436
Biosym Technologies, Inc.                      Fax. (518) 482-5433
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