[gmx-users] grompp gives no molecules were defined in the system
Hi, I have a problem with Gromacs. I want to do MD simulations with my proteïn in a DPPC-membrane. Therefore I followed Justin Lemkul's tutorial on membrane proteïn simulation. I just used a bigger membrane (256 lipids instead of 128). I managed to correctly embed the proteïn in the bilayer, I solvated it with genbox and then I want to add ions. But when I use grompp to get a .tpr file for genion, Gromacs fives the following error: Program grompp, VERSION 4.0.7 Source code file: ../../gromacs-4.0.7/src/kernel/grompp.c, line: 320 Fatal error: No molecules were defined in the system I did update my topology in the [ molecules ] section and checked it twice to see if it fits with the .gro file. It is correct, so I don't know what the problem is. Before the solvation there was no problem with grompp, so it must have something to do with the solvation? I hope someone can help me. Thanks, Marysa van den Berg _ Alles over Windows http://www.windows.nl/About.aspx-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] grompp gives no molecules were defined in the system
Hi Marysa, The error is about the definition of mulecules, which suggests that there are no [ moleculetype ] directives. Did you #include the proper .itp file(s) with the necessary moleculetype definitions? If not, you'll have to provide more information, probably posting the topology file itself. Cheers, Tsjerk On Thu, Jan 28, 2010 at 12:27 PM, Marysa van den Berg mvdberg1...@hotmail.com wrote: Hi, I have a problem with Gromacs. I want to do MD simulations with my proteïn in a DPPC-membrane. Therefore I followed Justin Lemkul's tutorial on membrane proteïn simulation. I just used a bigger membrane (256 lipids instead of 128). I managed to correctly embed the proteïn in the bilayer, I solvated it with genbox and then I want to add ions. But when I use grompp to get a .tpr file for genion, Gromacs fives the following error: Program grompp, VERSION 4.0.7 Source code file: ../../gromacs-4.0.7/src/kernel/grompp.c, line: 320 Fatal error: No molecules were defined in the system I did update my topology in the [ molecules ] section and checked it twice to see if it fits with the .gro file. It is correct, so I don't know what the problem is. Before the solvation there was no problem with grompp, so it must have something to do with the solvation? I hope someone can help me. Thanks, Marysa van den Berg Minder SPAM in de verbeterde Windows Live Hotmail -- gmx-users mailing list gmx-us...@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php -- Tsjerk A. Wassenaar, Ph.D. Computational Chemist Medicinal Chemist Neuropharmacologist -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] grompp gives no molecules were defined in the system
Do you have the right number of atoms indicated on the second line of the .gro file? What is in your [molecules] directive in your topology? -Justin Marysa van den Berg wrote: Hi, I have a problem with Gromacs. I want to do MD simulations with my proteïn in a DPPC-membrane. Therefore I followed Justin Lemkul's tutorial on membrane proteïn simulation. I just used a bigger membrane (256 lipids instead of 128). I managed to correctly embed the proteïn in the bilayer, I solvated it with genbox and then I want to add ions. But when I use grompp to get a .tpr file for genion, Gromacs fives the following error: /Program grompp, VERSION 4.0.7 Source code file: ../../gromacs-4.0.7/src/kernel/grompp.c, line: 320/ /Fatal error: No molecules were defined in the system / I did update my topology in the [ molecules ] section and checked it twice to see if it fits with the .gro file. It is correct, so I don't know what the problem is. Before the solvation there was no problem with grompp, so it must have something to do with the solvation? I hope someone can help me. Thanks, Marysa van den Berg Minder SPAM in de verbeterde Windows Live Hotmail http://mail.live.com -- 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/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/mailing_lists/users.php
RE: [gmx-users] grompp gives no molecules were defined in the system
Hi, The number of atoms in the second line of my .gro file are correct, I checked that. This is what my topology file says in the beginning: [ moleculetype ] ; Name nrexcl Protein 3 No changes here after the solvation. At the end after the [ atoms ] directive: ; Include Position restraint file #ifdef POSRES #include posre.itp #endif ; Strong po sition restraints for InflateGro #ifdef STRONG_POSRES #include strong_posre.itp endif ; Include DPPC chain topology #include dppc.itp ; Include water topology #include spc.itp #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcxfcy fcz 11 1000 1000 1000 #endif ; Include generic topology for ions #include ions.itp [ system ] ; Name Protein [ molecules ] ; Compound #mols Protein1 DPPC 242 SOL 48333 The only thing in the topology that changed after the solvation, was adding the watermolecules in the [ molecules ] section (SOL 48333) What could be the problem? Thanks, Marysa _ 25GB gratis online harde schijf http://skydrive.live.com-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] grompp gives no molecules were defined in the system
Marysa van den Berg wrote: Hi, The number of atoms in the second line of my .gro file are correct, I checked that. This is what my topology file says in the beginning: [ moleculetype ] ; Name nrexcl Protein 3 No changes here after the solvation. At the end after the [ atoms ] directive: ; Include Position restraint file #ifdef POSRES #include posre.itp #endif ; Strong po sition restraints for InflateGro #ifdef STRONG_POSRES #include strong_posre.itp endif Here's the problem. To end the #ifdef statement, you need #endif, not endif. Since you haven't closed the #ifdef, nothing is being found after this point in the topology (assuming you're not specifying define = -DSTRONG_POSRES in the .mdp file, which you only want at certain times). -Justin ; Include DPPC chain topology #include dppc.itp ; Include water topology #include spc.itp #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcxfcy fcz 11 1000 1000 1000 #endif ; Include generic topology for ions #include ions.itp [ system ] ; Name Protein [ molecules ] ; Compound #mols Protein1 DPPC 242 SOL 48333 The only thing in the topology that changed after the solvation, was adding the watermolecules in the [ molecules ] section (SOL 48333) What could be the problem? Thanks, Marysa Ontdek nu Windows phone. De smartphone van dit moment http://www.microsoft.com/windowsmobile/nl-nl/default.mspx -- 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/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/mailing_lists/users.php
