Re: [gmx-users] Energy minimization of an UNKNOWN molecule.
On 11/3/14 12:57 AM, Kalyanashis Jana wrote: Thank you very much... But I am not going to use any parent molecules like protein or DNA. I would like to perform the gromacs simulation for this unknown molecule. First few lines of my topology file.. ; ; File 'topol.top' was generated ; By user: kollan (506) ; On host: master.localdomain ; At date: Sun Nov 2 20:28:10 2014 ; ; This is a standalone topology file ; ; It was generated using program: ; pdb2gmx - VERSION 4.6.3 ; ; Command line was: ; pdb2gmx -f A-T.pdb -o A-T1.pdb -p topol.top ; ; Force field was read from the standard Gromacs share directory. ; ; Include forcefield parameters # include A-T.itp ; ; Built itp for A-T.mol2 ;by user vzoete Mon Oct 27 06:32:46 CET 2014 ; ; [ atomtypes ] The yellow colored lines are first seven line A-T.itp file And the error was Fatal error: Syntax error - File A-T.itp, line 7 Last line read: '[ atomtypes ]' Invalid order for directive atomtypes Please help me.. You'll need to show us what is in A-T.itp, because that's where the problem is. Probably you're missing a [defaults] directive, but that's just a guess. -Justin On Mon, Nov 3, 2014 at 1:28 AM, Justin Lemkul jalem...@vt.edu wrote: On 11/2/14 11:32 AM, Kalyanashis Jana wrote: Thank you so much... I have tried to run the grompp step according to you. But it is showing Fatal error: Syntax error - File A-T.itp, line 7 Last line read: '[ atomtypes ]' Invalid order for directive atomtypes I have attached the .itp file and .top file. Please kindly tell me, what to do now.. Force-field level directives must be declared before molecule-level directives. So if your ligand requires new bonded or nonbonded parameters, or new atom types, it must be #included before the declaration of any [moleculetype]. So put your #include statement for the ligand topology immediately after the #include statement for the parent force field. -Justin On Sun, Nov 2, 2014 at 9:15 PM, Victor Rosas Garcia rosas.vic...@gmail.com wrote: just put the itp file in your working directory, and include it in the top file of your system, so that Gromacs can find it. Hope this helps. Victor 2014-11-02 8:54 GMT-06:00 Kalyanashis Jana kalyan.chem...@gmail.com: Dear all, I am trying to run a gromacs simulation using an .itp file of an unknown molecule ( non protein and DNA). I don't want to put the .itp file in a forcefield folder and I would like put it in my working directory. Can you please tell me, what is procedure to finish the energy minimization? Please help me.. Thanks in advance, Kalyanashis -- Kalyanashis Jana email: kalyan.chem...@gmail.com -- 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. -- == 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 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- 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. 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 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- 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.
[gmx-users] Energy minimization of an UNKNOWN molecule.
Dear all, I am trying to run a gromacs simulation using an .itp file of an unknown molecule ( non protein and DNA). I don't want to put the .itp file in a forcefield folder and I would like put it in my working directory. Can you please tell me, what is procedure to finish the energy minimization? Please help me.. Thanks in advance, Kalyanashis -- Kalyanashis Jana email: kalyan.chem...@gmail.com -- 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] Energy minimization of an UNKNOWN molecule.
just put the itp file in your working directory, and include it in the top file of your system, so that Gromacs can find it. Hope this helps. Victor 2014-11-02 8:54 GMT-06:00 Kalyanashis Jana kalyan.chem...@gmail.com: Dear all, I am trying to run a gromacs simulation using an .itp file of an unknown molecule ( non protein and DNA). I don't want to put the .itp file in a forcefield folder and I would like put it in my working directory. Can you please tell me, what is procedure to finish the energy minimization? Please help me.. Thanks in advance, Kalyanashis -- Kalyanashis Jana email: kalyan.chem...@gmail.com -- 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] Energy minimization of an UNKNOWN molecule.
Thank you so much... I have tried to run the grompp step according to you. But it is showing Fatal error: Syntax error - File A-T.itp, line 7 Last line read: '[ atomtypes ] ' Invalid order for directive atomtypes I have attached the .itp file and .top file. Please kindly tell me, what to do now.. On Sun, Nov 2, 2014 at 9:15 PM, Victor Rosas Garcia rosas.vic...@gmail.com wrote: just put the itp file in your working directory, and include it in the top file of your system, so that Gromacs can find it. Hope this helps. Victor 2014-11-02 8:54 GMT-06:00 Kalyanashis Jana kalyan.chem...@gmail.com: Dear all, I am trying to run a gromacs simulation using an .itp file of an unknown molecule ( non protein and DNA). I don't want to put the .itp file in a forcefield folder and I would like put it in my working directory. Can you please tell me, what is procedure to finish the energy minimization? Please help me.. Thanks in advance, Kalyanashis -- Kalyanashis Jana email: kalyan.chem...@gmail.com -- 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. -- Kalyanashis Jana email: kalyan.chem...@gmail.com -- 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] Energy minimization of an UNKNOWN molecule.
On 11/2/14 11:32 AM, Kalyanashis Jana wrote: Thank you so much... I have tried to run the grompp step according to you. But it is showing Fatal error: Syntax error - File A-T.itp, line 7 Last line read: '[ atomtypes ]' Invalid order for directive atomtypes I have attached the .itp file and .top file. Please kindly tell me, what to do now.. Force-field level directives must be declared before molecule-level directives. So if your ligand requires new bonded or nonbonded parameters, or new atom types, it must be #included before the declaration of any [moleculetype]. So put your #include statement for the ligand topology immediately after the #include statement for the parent force field. -Justin On Sun, Nov 2, 2014 at 9:15 PM, Victor Rosas Garcia rosas.vic...@gmail.com wrote: just put the itp file in your working directory, and include it in the top file of your system, so that Gromacs can find it. Hope this helps. Victor 2014-11-02 8:54 GMT-06:00 Kalyanashis Jana kalyan.chem...@gmail.com: Dear all, I am trying to run a gromacs simulation using an .itp file of an unknown molecule ( non protein and DNA). I don't want to put the .itp file in a forcefield folder and I would like put it in my working directory. Can you please tell me, what is procedure to finish the energy minimization? Please help me.. Thanks in advance, Kalyanashis -- Kalyanashis Jana email: kalyan.chem...@gmail.com -- 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. -- == 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 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- 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] Energy minimization of an UNKNOWN molecule.
Thank you very much... But I am not going to use any parent molecules like protein or DNA. I would like to perform the gromacs simulation for this unknown molecule. First few lines of my topology file.. ; ; File 'topol.top' was generated ; By user: kollan (506) ; On host: master.localdomain ; At date: Sun Nov 2 20:28:10 2014 ; ; This is a standalone topology file ; ; It was generated using program: ; pdb2gmx - VERSION 4.6.3 ; ; Command line was: ; pdb2gmx -f A-T.pdb -o A-T1.pdb -p topol.top ; ; Force field was read from the standard Gromacs share directory. ; ; Include forcefield parameters # include A-T.itp ; ; Built itp for A-T.mol2 ;by user vzoete Mon Oct 27 06:32:46 CET 2014 ; ; [ atomtypes ] The yellow colored lines are first seven line A-T.itp file And the error was Fatal error: Syntax error - File A-T.itp, line 7 Last line read: '[ atomtypes ]' Invalid order for directive atomtypes Please help me.. On Mon, Nov 3, 2014 at 1:28 AM, Justin Lemkul jalem...@vt.edu wrote: On 11/2/14 11:32 AM, Kalyanashis Jana wrote: Thank you so much... I have tried to run the grompp step according to you. But it is showing Fatal error: Syntax error - File A-T.itp, line 7 Last line read: '[ atomtypes ]' Invalid order for directive atomtypes I have attached the .itp file and .top file. Please kindly tell me, what to do now.. Force-field level directives must be declared before molecule-level directives. So if your ligand requires new bonded or nonbonded parameters, or new atom types, it must be #included before the declaration of any [moleculetype]. So put your #include statement for the ligand topology immediately after the #include statement for the parent force field. -Justin On Sun, Nov 2, 2014 at 9:15 PM, Victor Rosas Garcia rosas.vic...@gmail.com wrote: just put the itp file in your working directory, and include it in the top file of your system, so that Gromacs can find it. Hope this helps. Victor 2014-11-02 8:54 GMT-06:00 Kalyanashis Jana kalyan.chem...@gmail.com: Dear all, I am trying to run a gromacs simulation using an .itp file of an unknown molecule ( non protein and DNA). I don't want to put the .itp file in a forcefield folder and I would like put it in my working directory. Can you please tell me, what is procedure to finish the energy minimization? Please help me.. Thanks in advance, Kalyanashis -- Kalyanashis Jana email: kalyan.chem...@gmail.com -- 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. -- == 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 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- 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. -- Kalyanashis Jana email: kalyan.chem...@gmail.com -- 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.
