Hi Dan,
Thank you for your detailed answer.
Indeed, I have one of those scripts. But I would be happy to modify it
to extract more complete information ;-)
I understand that it is not possible to get both residue and atom
numbers so that the output could be similar to, say:
97(GLU_12.OE1+ASN_31.ND2+)
I will give a go to your suggested changes, thank you very much.
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 17:19, Daniel Roe a écrit :
> 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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Received on Tue May 28 2013 - 09:30:03 PDT
