Hi,
On Wed, Aug 24, 2016 at 12:04 PM, Indrajit Deb <biky2004indra.gmail.com> wrote:
> Dear Users and developers,
>
> Is it possible to identify/calculate solvent (waters/ions) bridge
> information within the same residue ?
Unfortunately no, not the way the bridging calculation is currently
implemented. I *think* you might be able to change this by changing
line 743 in Action_Hbond.cpp line 743 (GitHub code) from
if ( bridge->second.size() > 1) {
to
if ( bridge->second.size() >= 1) {
But I have not tested this so use at your own risk. This would be
something nice to have eventually but I have no timetable for when I
might be able to get to it.
Hope this helps,
-Dan
>
> 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
> residues.
>
> 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.
>
> Best,
> indrajit
>
>
> --------------------------------------------------------------------------------------------------------------
> *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 (
> R
> oom: 2.6.28
> ).
> Z. Noskowskiego Str. 12/14.
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> 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:
> +919239202278
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--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
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Received on Fri Aug 26 2016 - 13:30:02 PDT
