Hi,
The code records residue numbers and prints in this format to maintain
some backwards compatibility with ptraj (people may have scripts that
use this info). You could potentially modify the code to record atom
numbers instead of residue numbers. Note that I have *not* tested
these changes, so if you try them I would triple check your results to
make sure it actually works!
If you look at Action_Hbond.cpp in function DoAction() around line 501
where the 'if (calcSolvent_) {' block begins, look for references to
the variable 'solvent2solute'. Whenever this variable is accessed just
change references to residues to their corresponding atoms. For
example, lines 521-523 (in solute donor to solvent acceptor calc)
read:
int soluteres = (*CurrentParm_)[D].ResNum();
int solventmol = (*CurrentParm_)[*accept].ResNum();
solvent2solute[solventmol].insert( soluteres );
You can comment out the conversion to residue numbers and change the
solvent2solute line to use atom numbers instead:
//int soluteres = (*CurrentParm_)[D].ResNum();
//int solventmol = (*CurrentParm_)[*accept].ResNum();
solvent2solute[*accept].insert( D );
Similarly, you would have to change lines 546-548 (solvent donor to
solute acceptor). Then the print-out should have atom numbers instead
of residue numbers.
Note that these changes may also prevent future updates from being
applied cleanly so you may want to try this in a separate test
AmberTools directory. Good luck!
-Dan
On Tue, May 28, 2013 at 8:56 AM, Miguel Ortiz Lombardía
<miguel.ortiz-lombardia.afmb.univ-mrs.fr> wrote:
> 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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--
-------------------------
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 - 08:30:04 PDT
