Re: [gmx-users] AMBER99sb-ILDN force field and TIP4P water model
On Thu 28 Nov 2013 01:22:16 PM CET, Mahboobeh Eslami wrote: Hi GMX Users, please help me I am trying to begin a simulation of a protein and ligand coplex by gromacs4.6.3. I am using AMBER99sb-ILDN force field and TIP4P water model. However, I am facing a problem in the ion adding step. when I issue the grompp command to generate the necessary .tpr file for simulation to be utilised by genion tool, I get the following error : Fatal error: number of coordinates in coordinate file (solv.gro, 102546) does not match topology (topol.top, 133916) whe i use tip3p, i don't get error. Thank you very much Use share/gromacs/top/tip4p.gro when generating the simulation box, tip4p has an aditional interaction site best timo -- -- T.M.D. Graen Max Planck Institute for Biophysical Chemistry Theoretical and Computational Biophysics Department, 105 00 Am Fassberg 11 37077 Goettingen, Germany Tel.: ++49 551 201 2313 Fax: ++49 551 201 2302 Email: tgr...@gwdg.de -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] AMBER99sb-ILDN force field and TIP4P water model
Maybe you should modify your .tpr file manually according to what you added in the previous sections! On Thu, Nov 28, 2013 at 5:53 PM, Mahboobeh Eslami mahboobeh.esl...@yahoo.com wrote: dear timo Please send me further details. I'm not a professional. Thanks and regards On Thursday, November 28, 2013 4:28 PM, Timo Graen tgr...@gwdg.de wrote: On Thu 28 Nov 2013 01:22:16 PM CET, Mahboobeh Eslami wrote: Hi GMX Users, please help me I am trying to begin a simulation of a protein and ligand coplex by gromacs4.6.3. I am using AMBER99sb-ILDN force field and TIP4P water model. However, I am facing a problem in the ion adding step. when I issue the grompp command to generate the necessary .tpr file for simulation to be utilised by genion tool, I get the following error : Fatal error: number of coordinates in coordinate file (solv.gro, 102546) does not match topology (topol.top, 133916) whe i use tip3p, i don't get error. Thank you very much Use share/gromacs/top/tip4p.gro when generating the simulation box, tip4p has an aditional interaction site best timo -- -- T.M.D. Graen Max Planck Institute for Biophysical Chemistry Theoretical and Computational Biophysics Department, 105 00 Am Fassberg 11 37077 Goettingen, Germany Tel.: ++49 551 201 2313 Fax: ++49 551 201 2302 Email: tgr...@gwdg.de -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] AMBER99sb-ILDN force field and TIP4P water model
On 11/28/13 9:37 AM, Mohsen Ramezanpour wrote: Maybe you should modify your .tpr file manually according to what you added in the previous sections! Manually modify a .tpr? How would one do that? The OP needs to provide the exact commands issued. The fatal error shown results from poor bookkeeping (i.e. not making use of the -p option of genbox and genion) or use of the wrong water coordinate file. I would also suggest some basic tutorial material to become more familiar with simple Gromacs tasks. -Justin On Thu, Nov 28, 2013 at 5:53 PM, Mahboobeh Eslami mahboobeh.esl...@yahoo.com wrote: dear timo Please send me further details. I'm not a professional. Thanks and regards On Thursday, November 28, 2013 4:28 PM, Timo Graen tgr...@gwdg.de wrote: On Thu 28 Nov 2013 01:22:16 PM CET, Mahboobeh Eslami wrote: Hi GMX Users, please help me I am trying to begin a simulation of a protein and ligand coplex by gromacs4.6.3. I am using AMBER99sb-ILDN force field and TIP4P water model. However, I am facing a problem in the ion adding step. when I issue the grompp command to generate the necessary .tpr file for simulation to be utilised by genion tool, I get the following error : Fatal error: number of coordinates in coordinate file (solv.gro, 102546) does not match topology (topol.top, 133916) whe i use tip3p, i don't get error. Thank you very much Use share/gromacs/top/tip4p.gro when generating the simulation box, tip4p has an aditional interaction site best timo -- -- T.M.D. Graen Max Planck Institute for Biophysical Chemistry Theoretical and Computational Biophysics Department, 105 00 Am Fassberg 11 37077 Goettingen, Germany Tel.: ++49 551 201 2313 Fax: ++49 551 201 2302 Email: tgr...@gwdg.de -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- == 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 == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] AMBER99sb-ILDN force field and TIP4P water model
Oh, I am sorry, I made a big mistake! :) Best Regards On Thu, Nov 28, 2013 at 6:13 PM, Justin Lemkul jalem...@vt.edu wrote: On 11/28/13 9:37 AM, Mohsen Ramezanpour wrote: Maybe you should modify your .tpr file manually according to what you added in the previous sections! Manually modify a .tpr? How would one do that? The OP needs to provide the exact commands issued. The fatal error shown results from poor bookkeeping (i.e. not making use of the -p option of genbox and genion) or use of the wrong water coordinate file. I would also suggest some basic tutorial material to become more familiar with simple Gromacs tasks. -Justin On Thu, Nov 28, 2013 at 5:53 PM, Mahboobeh Eslami mahboobeh.esl...@yahoo.com wrote: dear timo Please send me further details. I'm not a professional. Thanks and regards On Thursday, November 28, 2013 4:28 PM, Timo Graen tgr...@gwdg.de wrote: On Thu 28 Nov 2013 01:22:16 PM CET, Mahboobeh Eslami wrote: Hi GMX Users, please help me I am trying to begin a simulation of a protein and ligand coplex by gromacs4.6.3. I am using AMBER99sb-ILDN force field and TIP4P water model. However, I am facing a problem in the ion adding step. when I issue the grompp command to generate the necessary .tpr file for simulation to be utilised by genion tool, I get the following error : Fatal error: number of coordinates in coordinate file (solv.gro, 102546) does not match topology (topol.top, 133916) whe i use tip3p, i don't get error. Thank you very much Use share/gromacs/top/tip4p.gro when generating the simulation box, tip4p has an aditional interaction site best timo -- -- T.M.D. Graen Max Planck Institute for Biophysical Chemistry Theoretical and Computational Biophysics Department, 105 00 Am Fassberg 11 37077 Goettingen, Germany Tel.: ++49 551 201 2313 Fax: ++49 551 201 2302 Email: tgr...@gwdg.de -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- == 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 == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/ Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] AMBER99sb-ILDN force field and TIP4P water model
Dear Justin I meant modifying .top file after adding some ions and water molecules which could be equivalent to -p option as you mentioned. What do you think about this? Please let me know On Thu, Nov 28, 2013 at 6:37 PM, Mohsen Ramezanpour ramezanpour.moh...@gmail.com wrote: Oh, I am sorry, I made a big mistake! :) Best Regards On Thu, Nov 28, 2013 at 6:13 PM, Justin Lemkul jalem...@vt.edu wrote: On 11/28/13 9:37 AM, Mohsen Ramezanpour wrote: Maybe you should modify your .tpr file manually according to what you added in the previous sections! Manually modify a .tpr? How would one do that? The OP needs to provide the exact commands issued. The fatal error shown results from poor bookkeeping (i.e. not making use of the -p option of genbox and genion) or use of the wrong water coordinate file. I would also suggest some basic tutorial material to become more familiar with simple Gromacs tasks. -Justin On Thu, Nov 28, 2013 at 5:53 PM, Mahboobeh Eslami mahboobeh.esl...@yahoo.com wrote: dear timo Please send me further details. I'm not a professional. Thanks and regards On Thursday, November 28, 2013 4:28 PM, Timo Graen tgr...@gwdg.de wrote: On Thu 28 Nov 2013 01:22:16 PM CET, Mahboobeh Eslami wrote: Hi GMX Users, please help me I am trying to begin a simulation of a protein and ligand coplex by gromacs4.6.3. I am using AMBER99sb-ILDN force field and TIP4P water model. However, I am facing a problem in the ion adding step. when I issue the grompp command to generate the necessary .tpr file for simulation to be utilised by genion tool, I get the following error : Fatal error: number of coordinates in coordinate file (solv.gro, 102546) does not match topology (topol.top, 133916) whe i use tip3p, i don't get error. Thank you very much Use share/gromacs/top/tip4p.gro when generating the simulation box, tip4p has an aditional interaction site best timo -- -- T.M.D. Graen Max Planck Institute for Biophysical Chemistry Theoretical and Computational Biophysics Department, 105 00 Am Fassberg 11 37077 Goettingen, Germany Tel.: ++49 551 201 2313 Fax: ++49 551 201 2302 Email: tgr...@gwdg.de -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- == 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 == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/ Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
