[gmx-users] Re: hydrogen bonds
vasilis.georgilas at BEST.eu.org
Sat Jul 31 00:59:51 CEST 2010
sorry for keep spamming you...
so i make 2 groups: acceptors and donors (with their hydrogen)
I hope now i am correct!
On Sat, Jul 31, 2010 at 1:55 AM, Justin A. Lemkul <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
>> 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
> and then with the g_hbond to do all the calculations.
>> 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>> 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.
>> 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.
>> 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> | (540) 231-9080
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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
> gmx-users mailing list gmx-users at gromacs.org
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the www interface
> or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Joint EoE Brno Coordinator
mail: vasilis.georgilas at BEST.eu.org
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