Hi Dan,
Thank you for your answer. Yes, that clarify my doubt.
Fer
On Tue, 28 May 2013 08:33:43 -0600, Daniel Roe wrote:
> 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
'(++...+),...''
>
> 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 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/ [1]
============================================== --
============================================== 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/ [2]
==============================================
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> -- ------------------------- 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/ [6] (801)
587-9652 (801) 585-9119 (Fax)
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[8]
--
==============================================
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/
==============================================
Links:
------
[1] http://fertoledo.wordpress.com/
[2]
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[3] mailto:AMBER.ambermd.org
[4]
http://lists.ambermd.org/mailman/listinfo/amber
[5]
mailto:fmgarcia.cbm.uam.es
[6] http://home.chpc.utah.edu/~cheatham/
[7]
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[8]
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Received on Tue May 28 2013 - 08:00:03 PDT
