[gmx-users] Ligand topology in topol.top
Hi Guys, I am using Charmm27 ff for my protein and ligand system. I used SwissParam to generate the topology for my ligand. I included the obtained topology of my ligand as in Justin tutorial: ; Include Position restraint file #ifdef POSRES #include posre.itp #endif ; Include ligand topology #include ligand.itp ; Ligand position restraints #ifdef POSRES #include posre_ligand.itp #endif ; Include water topology #include charmm27.ff/tip3p.itp When I wanted to run NVT I obtained: Fatal error: Syntax error - File egcg.itp, line 7 Last line read: '[ atomtypes ] ' Invalid order for directive atomtypes However when I included my topology as: ; Include forcefield parameters #include charmm27.ff/forcefield.itp #include ligand.itp [ moleculetype ] ; Name nrexc .. ; Include Position restraint file #ifdef POSRES #include posre.itp #endif ; Ligand position restraints #ifdef POSRES #include posre_egcg.itp #endif ; Include water topology #include charmm27.ff/tip3p.itp Everything seems to be ok! Any clue why is that? Regards, Steven -- 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] Ligand topology in topol.top
Steven Neumann wrote: Hi Guys, I am using Charmm27 ff for my protein and ligand system. I used SwissParam to generate the topology for my ligand. I included the obtained topology of my ligand as in Justin tutorial: ; Include Position restraint file #ifdef POSRES #include posre.itp #endif ; Include ligand topology #include ligand.itp ; Ligand position restraints #ifdef POSRES #include posre_ligand.itp #endif ; Include water topology #include charmm27.ff/tip3p.itp When I wanted to run NVT I obtained: Fatal error: Syntax error - File egcg.itp, line 7 Last line read: '[ atomtypes ] ' Invalid order for directive atomtypes However when I included my topology as: ; Include forcefield parameters #include charmm27.ff/forcefield.itp #include ligand.itp [ moleculetype ] ; Name nrexc .. ; Include Position restraint file #ifdef POSRES #include posre.itp #endif ; Ligand position restraints #ifdef POSRES #include posre_egcg.itp #endif ; Include water topology #include charmm27.ff/tip3p.itp Everything seems to be ok! Any clue why is that? The topology must follow a defined order. Please consult Chapter 5 of the manual for the required hierarchy. Of course, the latter case will also not work, because you've introduced ligand position restraints after the protein [moleculetype], so if invoked, they will cause a different fatal error. The Gromacs site also has more on these types of errors, as well as the list archive, where this error has been posted and solved hundreds of times. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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] Ligand topology in topol.top
On Tue, Nov 1, 2011 at 4:11 PM, Justin A. Lemkul jalem...@vt.edu wrote: Steven Neumann wrote: Hi Guys, I am using Charmm27 ff for my protein and ligand system. I used SwissParam to generate the topology for my ligand. I included the obtained topology of my ligand as in Justin tutorial: ; Include Position restraint file #ifdef POSRES #include posre.itp #endif ; Include ligand topology #include ligand.itp ; Ligand position restraints #ifdef POSRES #include posre_ligand.itp #endif ; Include water topology #include charmm27.ff/tip3p.itp When I wanted to run NVT I obtained: Fatal error: Syntax error - File egcg.itp, line 7 Last line read: '[ atomtypes ] ' Invalid order for directive atomtypes However when I included my topology as: ; Include forcefield parameters #include charmm27.ff/forcefield.itp #include ligand.itp [ moleculetype ] ; Name nrexc .. ; Include Position restraint file #ifdef POSRES #include posre.itp #endif ; Ligand position restraints #ifdef POSRES #include posre_egcg.itp #endif ; Include water topology #include charmm27.ff/tip3p.itp Everything seems to be ok! Any clue why is that? The topology must follow a defined order. Please consult Chapter 5 of the manual for the required hierarchy. Of course, the latter case will also not work, because you've introduced ligand position restraints after the protein [moleculetype], so if invoked, they will cause a different fatal error. The Gromacs site also has more on these types of errors, as well as the list archive, where this error has been posted and solved hundreds of times. -Justin Thank you Justin! But actually the last case I provided actually works... Steven -- 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] Ligand topology in topol.top
Steven Neumann wrote: On Tue, Nov 1, 2011 at 4:11 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: Steven Neumann wrote: Hi Guys, I am using Charmm27 ff for my protein and ligand system. I used SwissParam to generate the topology for my ligand. I included the obtained topology of my ligand as in Justin tutorial: ; Include Position restraint file #ifdef POSRES #include posre.itp #endif ; Include ligand topology #include ligand.itp ; Ligand position restraints #ifdef POSRES #include posre_ligand.itp #endif ; Include water topology #include charmm27.ff/tip3p.itp When I wanted to run NVT I obtained: Fatal error: Syntax error - File egcg.itp, line 7 Last line read: '[ atomtypes ] ' Invalid order for directive atomtypes However when I included my topology as: ; Include forcefield parameters #include charmm27.ff/forcefield.itp #include ligand.itp [ moleculetype ] ; Name nrexc .. ; Include Position restraint file #ifdef POSRES #include posre.itp #endif ; Ligand position restraints #ifdef POSRES #include posre_egcg.itp #endif ; Include water topology #include charmm27.ff/tip3p.itp Everything seems to be ok! Any clue why is that? The topology must follow a defined order. Please consult Chapter 5 of the manual for the required hierarchy. Of course, the latter case will also not work, because you've introduced ligand position restraints after the protein [moleculetype], so if invoked, they will cause a different fatal error. The Gromacs site also has more on these types of errors, as well as the list archive, where this error has been posted and solved hundreds of times. -Justin Thank you Justin! But actually the last case I provided actually works... Then the position restraints are not being applied to the ligand. They can't be. Once the protein [moleculetype] is introduced, all [position_restraints] directives immediately after are applied to it. Try invoking the restraints separately, i.e. with define = -DPOSRES -DPOSRES_LIGAND and you will get a fatal error. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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] Ligand topology in topol.top
On Tue, Nov 1, 2011 at 5:44 PM, Justin A. Lemkul jalem...@vt.edu wrote: Steven Neumann wrote: On Tue, Nov 1, 2011 at 4:11 PM, Justin A. Lemkul jalem...@vt.edumailto: jalem...@vt.edu wrote: Steven Neumann wrote: Hi Guys, I am using Charmm27 ff for my protein and ligand system. I used SwissParam to generate the topology for my ligand. I included the obtained topology of my ligand as in Justin tutorial: ; Include Position restraint file #ifdef POSRES #include posre.itp #endif ; Include ligand topology #include ligand.itp ; Ligand position restraints #ifdef POSRES #include posre_ligand.itp #endif ; Include water topology #include charmm27.ff/tip3p.itp When I wanted to run NVT I obtained: Fatal error: Syntax error - File egcg.itp, line 7 Last line read: '[ atomtypes ] ' Invalid order for directive atomtypes However when I included my topology as: ; Include forcefield parameters #include charmm27.ff/forcefield.itp #include ligand.itp [ moleculetype ] ; Name nrexc .. ; Include Position restraint file #ifdef POSRES #include posre.itp #endif ; Ligand position restraints #ifdef POSRES #include posre_egcg.itp #endif ; Include water topology #include charmm27.ff/tip3p.itp Everything seems to be ok! Any clue why is that? The topology must follow a defined order. Please consult Chapter 5 of the manual for the required hierarchy. Of course, the latter case will also not work, because you've introduced ligand position restraints after the protein [moleculetype], so if invoked, they will cause a different fatal error. The Gromacs site also has more on these types of errors, as well as the list archive, where this error has been posted and solved hundreds of times. -Justin Thank you Justin! But actually the last case I provided actually works... Then the position restraints are not being applied to the ligand. They can't be. Once the protein [moleculetype] is introduced, all [position_restraints] directives immediately after are applied to it. Try invoking the restraints separately, i.e. with define = -DPOSRES -DPOSRES_LIGAND and you will get a fatal error. -Justin You are as always right :) Thanks! Steven -- 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
