Hi,
As stated in the description of the 'hbond' command in the AT13 manual
(Chapter 8.10.18):
'...as well as the residue # of the bridging solvent and the solute
residues being bridged with format ’<solvent resnum>(<solute
res1>+<solute res2>+...+),...’'
So in your case:
> 97(12+31+),639(16+27+),1933(4+39+),5244(20+23+),7381(10+33+),10415(9+34+),10964(6+37+),
means solvent residue 97 is bridging solute residues 12 and 31 (i.e.
in that coordinate frame solvent is h-bonding to both solute residues
at the same time), solvent residue 639 is bridging solute residues 16
and 27, etc. Hope this helps clarify things.
-Dan
On Tue, May 28, 2013 at 8:06 AM, Fernando Martín García
<fmgarcia.cbm.uam.es> wrote:
>
>
> Dear Amber users,
>
> I'm trying to find some hydrogen bonds between
> DNA and the spine water that it's found in minor groove. I have one
> question about hbond command in cpptraj (version 13.1). I'm using
> following line:
>
> hbond solventhb ID out ${MOL}.hbonds :1-42.N3,O2
> series solventdonor :WAT.O
>
> In out file, I get this output format:
>
> 1
> 0 31 7
> 97(12+31+),639(16+27+),1933(4+39+),5244(20+23+),7381(10+33+),10415(9+34+),10964(6+37+),
>
>
> is this mean that oxygen atom 97 is forming two bonds with bases 12
> and 31 (for example) in the same frame with the corresponding atoms, or
> only a single one with the atom of 12 or 31? Is there any way to see if
> is forming one or two bonds with the atoms of the base pair?
>
> I know is
> simply question, but I need to clarify this for my results.
>
> Thank you
> in advance.
>
> Best regards,
>
> Fernando
>
> --
>
> ==============================================
> Fernando Martín
> García
> Molecular Modeling Group - Lab 312.1
> Molecular Biology
> Center "Severo Ochoa"
> C/ Nicolás Cabrera, 1.
> UAM University.
> Cantoblanco, 28049 Madrid. Spain.
> TEL: (+34) 91-196-4662 FAX: (+34)
> 91-196-4420
> Web:
> http://fertoledo.wordpress.com/
> ==============================================
>
> --
>
> ==============================================
> Fernando Martín
> García
> Molecular Modeling Group - Lab 312.1
> Molecular Biology
> Center "Severo Ochoa"
> C/ Nicolás Cabrera, 1.
> UAM University.
> Cantoblanco, 28049 Madrid. Spain.
> TEL: (+34) 91-196-4662 FAX: (+34)
> 91-196-4420
> Web:
> http://fertoledo.wordpress.com/
> ==============================================
>
>
> _______________________________________________
> 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 201
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-9119 (Fax)
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Received on Tue May 28 2013 - 08:00:03 PDT
