Hi Dan,
Would it be feasible for the solute residues bridged to know which are
the atoms that are concerned by the water bridge? Of course, one could
get this information knowing the frame number and the solvent and
residues involved, but it would seem easier to get all the information
in one shot.
Cheers,
Miguel Ortiz Lombardía
Architecture et Fonction des Macromolécules Biologiques (UMR7257)
CNRS, Aix-Marseille Université
Case 932, 163 Avenue de Luminy, 13288 Marseille cedex 9, France
Tel: +33(0) 491 82 55 93
Fax: +33(0) 491 26 67 20
mailto:
miguel.ortiz-lombardia.afmb.univ-mrs.fr
http://www.afmb.univ-mrs.fr/Miguel-Ortiz-Lombardia
Le 28/05/13 16:33, Daniel Roe a écrit :
> 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
>
>
>
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Received on Tue May 28 2013 - 08:00:05 PDT
