[gmx-users] g_hbond for trajectory without having box information
jalemkul at vt.edu
Fri Jul 19 11:13:55 CEST 2013
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
> 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.
> 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
>>>> individual snapshots from MD simulation, but because this trajectory does
>>>> not have the coordinates/information for simulation box, g_hbond is
>>>> 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.
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
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