You can probably get the results you want by using the
'donormask'/'donorhmask'/'acceptormask' keywords of the 'hbond'
command to specify only residues/atoms involved in salt bridges. Also,
if all you are interested in is interactions between the protein and
RNA use the 'nointramol' keyword so that you get only intermolecular
interactions.
-Dan
On Sat, Jul 30, 2016 at 1:27 AM, Muthukumaran R <kumaran.bicpu.edu.in> wrote:
> Dear users,
>
> I am working protein RNA complexes and I like to calculate the number of
> salt bridges formed between RNA and protein.
>
> I went through Hydrogen bond analysis by Daniel R. Roe
> (http://www.amber.utah.edu/AMBER-workshop/London-2015/Hbond/)
>
> I calculated the water mediated interactions using
>
> hbond hb1 :1-236 out list.out avgout avg.out solventdonor :WAT.O
> solventacceptor :WAT.O solvout sol_list.out bridgeout orf_bridge.out
>
> similarly I like to calculate salt bridges between protein RNA.
>
> It will be greatly helpful with suggestions in this regards.
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Mon Aug 01 2016 - 10:30:03 PDT
