[gmx-users] Water mediated hydrogen bonding

[suhani nagpal]

Oh! Yes yes. Thanks for the same.

After command -f  -s   -n  -hbm -hbn -num -dist :

Select a group: 19
Selected 19: 'SOL_&_OW'
Select a group: 18
Selected 18: 'r_38-57'
Checking for overlap in atoms between SOL_&_OW and r_38-57
Calculating contacts between SOL_&_OW (9468 atoms) and r_38-57 (268 atoms)
Found 268 donors and 9468 acceptors
Making hbmap structure...done.
Reading frame       0 time    0.000
Will do grid-seach on 11x11x8 grid, rcut=0.55
Frame loop parallelized with OpenMP using 16 threads.

is this seems alright? because it has not started to read frames.

Also, are there important identifiers to be used in the command?


I meant there is 'Here' hyperlink' on this page (
http://www.gromacs.org/Documentation/Gromacs_Utilities/g_hbond). It shows
not found.







On Thu, Jan 15, 2015 at 7:03 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 1/15/15 8:31 AM, suhani nagpal wrote:
>
>> Greetings
>>
>> I want to calculate hydrogen bonds between solvent molecules and a set of
>> residues.
>>
>> For that I have created an Index file with:
>>
>> 13 (sol) & a OW   (group 1)
>>
>> r 1-10 & a H         (group 2)
>>
>>
>> But the g_hbond shows error - nothing to be done if I give -num and If I
>> give -contact, it does start but fails to read frames.
>>
>> Kindly suggest the right approach to evaluate hydrogen bonding between
>> solvent molecules and protein residues.
>>
>>
> Your index groups are created incorrectly.  If group 2 only has H, the
> heavy atom in the donor is absent, so g_hbond cannot work.  If you want to
> analyze H-bonds between water and residues 1-10, you just need
>
> r 1-10
>
> for make_ndx.  g_hbond figures out which chemical groups participate on
> its own.
>
>  I also tried reading
>> http://www.gromacs.org/Documentation/Gromacs_Utilities/g_hbond - it does
>> not open.
>>
>>
> Works for me.
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
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