[gmx-users] g_hbond for trajectory without having box information

[Justin Lemkul]

On 7/19/13 4:17 AM, bipin singh wrote:
> According to the suggestion I added the box to the trajectory using -box
> option of trjconv, using the following commands:
>
> trjconv -f traj.xtc -s md.tpr -box 0.9 0.9 0.9 -o traj_box.xtc
>
> then using the g_hbond on the output trjectory (traj_box.xtc) run
> successfully but gives the wrong number of H-bonds between the proteins
> atoms.
>
> I have also tried to process the output trajectory (traj_box.xtc) with
> trjconv using -pbc mol -ur compact options before using g_hbond, but again
> I have got wrong number of H-bonds.
>
> Please help me to rectify the error.
>

A 0.9-nm cubic box is likely too small to correctly accommodate even an amino 
acid, let alone an entire protein.

-Justin

>
> On Fri, Jul 19, 2013 at 11:19 AM, bipin singh <bipinelmat at gmail.com> wrote:
>
>> Thanks a lot Prof. David. I will try this.
>>
>>
>> On Fri, Jul 19, 2013 at 10:45 AM, David van der Spoel <
>> spoel at xray.bmc.uu.se> wrote:
>>
>>> On 2013-07-19 06:26, bipin singh wrote:
>>>
>>>> Hello all,
>>>>
>>>> I was using g_hbond to calculate H-bonds for a trajectory made from
>>>> several
>>>> individual snapshots from MD simulation, but because this trajectory does
>>>> not have the coordinates/information for simulation box, g_hbond is
>>>> giving
>>>> the following error:
>>>>
>>>> Fatal error:
>>>> Your computational box has shrunk too much.
>>>> g_hbond_mpi can not handle this situation, sorry.
>>>>
>>>>
>>>> Please let me know, if there is any way to rectify this error.
>>>>
>>>>
>>>>   you can add a box to your trajectory using trjconv.
>>>
>>> --
>>> David van der Spoel, Ph.D., Professor of Biology
>>> Dept. of Cell & Molec. Biol., Uppsala University.
>>> Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
>>> spoel at xray.bmc.uu.se    http://folding.bmc.uu.se
>>> --
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>>
>>
>>
>> --
>> *-----------------------
>> Thanks and Regards,
>> Bipin Singh*
>>
>
>
>

-- 
==================================================

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441

==================================================