Re: [gmx-users] g_hbond for trajectory without having box information
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. On Fri, Jul 19, 2013 at 11:19 AM, bipin singh bipinel...@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 sp...@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. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- *--- Thanks and Regards, Bipin Singh* -- *--- Thanks and Regards, Bipin Singh* -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] g_hbond for trajectory without having box information
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 bipinel...@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 sp...@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. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- *--- 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 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] g_hbond for trajectory without having box information
Sorry for my silly mistake. I have a doubt regarding the expected difference in total No. of H-bonds calculated with whole a MD trajectory (protein+solvent box) and H-bonds calculated with concatenated frames (only protein) from a MD trajectory. I mean, will the number of H-bonds present at a particular time in a MD trajectory (protein+solvent), should be exactly same as number of H-bonds calculated using trajectory made of concatenated frames (only protein) from (if we look at number of H-bonds present at same point of time in both). Because I am not getting the exact match between the two, there is random difference of 1-3 H-bonds at some point of time. On Fri, Jul 19, 2013 at 2:43 PM, Justin Lemkul jalem...@vt.edu wrote: 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 bipinel...@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 sp...@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. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-usershttp://lists.gromacs.org/**mailman/listinfo/gmx-users htt**p://lists.gromacs.org/mailman/**listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchh**ttp://www.gromacs.org/Support/** Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Listshttp://www.gromacs.org/**Support/Mailing_Lists http://**www.gromacs.org/Support/**Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- *--- 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@outerbanks.umaryland.**edu jalem...@outerbanks.umaryland.edu | (410) 706-7441 ==** -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- *--- Thanks and Regards, Bipin Singh* -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] g_hbond for trajectory without having box information
On 7/19/13 6:55 AM, bipin singh wrote: Sorry for my silly mistake. I have a doubt regarding the expected difference in total No. of H-bonds calculated with whole a MD trajectory (protein+solvent box) and H-bonds calculated with concatenated frames (only protein) from a MD trajectory. I mean, will the number of H-bonds present at a particular time in a MD trajectory (protein+solvent), should be exactly same as number of H-bonds calculated using trajectory made of concatenated frames (only protein) from (if we look at number of H-bonds present at same point of time in both). Because I am not getting the exact match between the two, there is random difference of 1-3 H-bonds at some point of time. I suspect that the issue stems from having to manually set the box. I don't understand why you would have to do this after running a simulation in explicit solvent. Did you just extract the protein coordinates from the explicit simulation? If so, I don't see how the box information would be omitted. You can get spurious H-bonds across PBC if you are manually setting a bad box size in a given frame or series of frames. Without the exact sequence of commands from what you have done, it's pure guesswork. -Justin On Fri, Jul 19, 2013 at 2:43 PM, Justin Lemkul jalem...@vt.edu wrote: 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 bipinel...@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 sp...@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. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-usershttp://lists.gromacs.org/**mailman/listinfo/gmx-users htt**p://lists.gromacs.org/mailman/**listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchh**ttp://www.gromacs.org/Support/** Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Listshttp://www.gromacs.org/**Support/Mailing_Lists http://**www.gromacs.org/Support/**Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- *--- 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@outerbanks.umaryland.**edu jalem...@outerbanks.umaryland.edu | (410) 706-7441 ==** -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health
[gmx-users] g_hbond for trajectory without having box information
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. -- *--- Thanks and Regards, Bipin Singh* -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] g_hbond for trajectory without having box information
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. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] g_hbond for trajectory without having box information
Thanks a lot Prof. David. I will try this. On Fri, Jul 19, 2013 at 10:45 AM, David van der Spoel sp...@xray.bmc.uu.sewrote: 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. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- *--- Thanks and Regards, Bipin Singh* -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
