[gmx-users] g_hbond on trajectory

[Jennifer Vo]

Thank you, Justin.
Jennifer


On Tue, Jun 2, 2015 at 2:09 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 6/2/15 5:01 AM, Jennifer Vo wrote:
>
>> Dear All,
>> I used g_hbond to analyze the possible hydrogen bonds between protein and
>> solvent (water) over the trajectory with this command:
>> g_hbond -s md-1.tpr -f md.xtc -n index.ndx -hbm hbmap.xpm -num hbnum.xvg
>> -g
>> hbond.log -dist hbdist.xvg -nhbdist nhbdist.xvg
>>
>> The log file showed me:
>> ....
>>    SER141OG      SER141HG     SOL2920OW
>>    SER141OG      SER141HG     SOL4449OW
>>    SER141OG      SER141HG     SOL5073OW
>>    SER141OG      SER141HG     SOL11886OW
>>    SER141OG      SER141HG     SOL13715OW
>> ....
>> I wonder if this calculation is based on one coordinate file (if yes,
>> which
>> one!?) or the average structure over trajectory?
>>
>
> Trajectory analysis is done for every frame in the trajectory.  The log
> output just indicates that different waters were hydrogen bonded to that
> particular Ser at different times.
>
> -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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