[gmx-users] Re: hydrogen bonds
Justin A. Lemkul
jalemkul at vt.edu
Sat Jul 31 01:00:58 CEST 2010
Vasilis Georgilas wrote:
> sorry for keep spamming you...
>
> so i make 2 groups: acceptors and donors (with their hydrogen)
>
> I hope now i am correct!
>
One way to find out... :)
-Justin
>
> On Sat, Jul 31, 2010 at 1:55 AM, Justin A. Lemkul <jalemkul at vt.edu
> <mailto:jalemkul at vt.edu>> wrote:
>
>
>
> Vasilis Georgilas wrote:
>
> I didn't get why the command i propsed won't work.
>
>
> Because you typed:
>
> a HO a OM a O
>
> I assumed you meant you would actually try this with make_ndx. It
> is wrong for several reasons, the most immediate of which is the use
> of "a" with atom types. To use "a" you must supply atom *names* not
> types. If you want to specify any selections based on types, you
> must provide a .tpr file as input and use "t" instead of "a."
>
>
> My idea, according what you proposed, is to use make_ndx and
> then make 3 groups:
>
> oxygen with the doble bond, oxyegn of carboxyle and hydroxele
>
>
> These groups sound almost correct, but they do not correspond to
> what you typed before. You can't specify the hydrogen as its own
> group, since it won't be connected to its donor atom (O4). To
> specify the hydroxyl, for example, what you want is:
>
> a H2 | a O4
>
> -Justin
>
> and then with the g_hbond to do all the calculations.
>
> Right??
>
> thank you once again for the help
>
> On Fri, Jul 30, 2010 at 8:19 PM, Justin A. Lemkul
> <jalemkul at vt.edu <mailto:jalemkul at vt.edu>
> <mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>>> wrote:
>
>
>
> Vasilis Georgilas wrote:
>
> This is from my topology file for palmitic acid.
>
> You say a should make a group of all O, of OM and of HO.
>
> But for the calculation I need the angle between hydrogene -
> donor - acceptor.
> So my index file should be in triplets, right?? this means I
> should type a HO a OA a O.
>
> Correct?
>
>
> No. The donor and acceptor groups should be separate. The
> geometry
> is easily calculated from O-H...O coordinates. You should
> also not
> have a group for just hydrogen, you need the group to contain the
> relevant functional group, which is the hydroxyl in this case
> (atoms
> H2 and O4 in a single group).
>
> Also note that your proposed command will not work. To select by
> atom type (i.e., HO, OA, and O) you need to provide a .tpr
> file as
> input to make_ndx and use "t HO" etc. Otherwise, select by
> atom name.
>
> -Justin
>
>
> thank you
>
>
> [ atoms ]
> ; nr type resnr residu atom cgnr
> charge 1 HO 1 PLM H2 1
> 0.370 2 OM 1 PLM O4
> 1 -0.460 3
> C 1 PLM C3 1 0.42
> 4 O 1 PLM O5 1 -0.45
> 5 CP2 1 PLM C4 2 0.12
> 6 CP2
> 1 PLM C5 3 0 7 CP2
> 1
> PLM C6 4 0 8 CP2 1
> PLM C7 5 0
> 9 CP2 1 PLM C8 6 0
> 10 CP2 1 PLM C9 7 0
> 11 CP2 1 PLM C10 8 0
> 12 CP2 1 PLM C11 9 0
> 13 CP2 1 PLM C12 10 0
> 14 CP2 1 PLM C13 11 0
> 15 CP2 1 PLM C14 12 0
> 16 CP2 1 PLM C15 13 0
> 17 CP2 1 PLM C16 14 0
> 18 CP2 1 PLM C17 15 0
> 19 CP3 1 PLM C18 16 0
>
>
> -- ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu <http://vt.edu> <http://vt.edu> | (540)
> 231-9080
>
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
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> --
> Vasilis Georgilas
> LBG Patra
> Joint EoE Brno Coordinator
> mail: vasilis.georgilas at BEST.eu.org
> <mailto:vasilis.georgilas at BEST.eu.org>
> <mailto:vasilis.georgilas at BEST.eu.org
> <mailto:vasilis.georgilas at BEST.eu.org>>
> mobile: +306973041057
>
>
> --
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
> --
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> Please search the archive at http://www.gromacs.org/search before
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>
>
>
> --
> Vasilis Georgilas
> LBG Patra
> Joint EoE Brno Coordinator
> mail: vasilis.georgilas at BEST.eu.org <mailto:vasilis.georgilas at BEST.eu.org>
> mobile: +306973041057
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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