[AMBER] Regarding hbond bridgeout

From: Indrajit Deb <biky2004indra.gmail.com>
Date: Wed, 24 Aug 2016 18:04:17 +0200

Dear Users and developers,

Is it possible to identify/calculate solvent (waters/ions) bridge
information within the same residue ?

Actually from grid analysis I can clearly see the water bridging between
the OP2 and specific base atom within a modified RNA residues in a duplex.

Also there are bridging waters between the OP2 atoms of two consecutive

The 'hbond bridgeout' command is writing the information on bridging waters
between two consecutive residues but not writing the information when the
bridge is within the same residue label.


*Indrajit Deb*
alternate emails: indrajitdeb81.gmail.com, idbmbg_s.caluniv.ac.in
*Present Position*
International Centre for Genetic Engineering and Biotechnology (ICGEB,
Italy) SMART Fellow,
Department of Structural Chemistry and Biology of Nucleic Acids,
Institute of Bioorganic Chemistry (IBCh),
Polish Academy of Sciences (PAS).
European Center for Bioinformatics and Genomics (ECBiG) Campus (
oom: 2.6.28
Z. Noskowskiego Str. 12/14.
Poznan 61-704, Poland​.
Phone: +48616653042, ​Personal Mobile: +48662513522​

*Previous Position*​
Ph.D Student,
Department of Biophysics, Molecular Biology and Bioinformatics, University
of Calcutta (CU), 92 APC Road, Kolkata - 700009, India. Phone:
+913323508386 (extn. 329, 321), Fax: +913323519755. Personal Mobile:
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Received on Wed Aug 24 2016 - 09:30:03 PDT
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