[AMBER] Bridging Sodium ions using hbond

From: DEBOSTUTI GHOSHDASTIDAR <debostutighosh.gmail.com>
Date: Mon, 1 Sep 2014 16:06:28 +0530

Dear Amber Users,

I am trying to find out the Na+ ions that bridge the *phosphate* groups of
A-DNA. Following is my command:

hbond out test1.dat solventdonor :Na+ solventacceptor :1-24.O1P,O2P
nointramol solvout test.dat (where 1-24 are the residue numbers of the DNA

In the output, however, I see that test.dat contains not only hbond
information between the O1P/O2P with Na+, but also those formed between
other atoms of the DNA and Na+.

Hence, I assume that the information on solvent bridges given in the
test1.dat file include Na+ ions that bridge any two atoms of the DNA and
not just the phosphates.

Any suggestions on how I can get the required information, i.e, only Na+
ions that bridge the phosphates?

Debostuti Ghosh Dastidar
Department of Biotechnology
Indian Institute of Technology Madras
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Received on Mon Sep 01 2014 - 04:00:02 PDT
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