Re: [gmx-users] Protein ligand molecular dynamics simulation
Hi Justin, I generated topologies of my protein using PDB2GMX (charmm27 FF) and ligand topology using swissparam tool using Charmm force field i included ligand.itp file in topol.top of protein. And i used docked complex structure (protein + ligand) from docking analysis and generated boxed.pdb next i created solvated.pdb using (editconf and genbox tools) and also checked SOL molecules updated in topol.top file next i checked solvated.pdb file in pymol my ligand is in correct place in protein the way i wanted but problem came after this while using grompp I used grompp tool to minimize this solvated.pdb it is showing following error..using em.mdp Fatal Error number of coordinates in coordinate file (solvated.pdb, 51540) does not match topology (topol.top, 52756) I know this is commonly known issue for new users of gromacs. I looked up in gmx-archive list couldnt find optimal solution for my problem.. Let me know how to solve this ...issue... Cheers, Nitin On Mon, Apr 16, 2012 at 5:03 PM, Justin A. Lemkul jalem...@vt.edu wrote: sai nitin wrote: Hi all, I have done complex (protein + ligand) complex from autodock software using this complex im trying to follow http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin/** gmx-tutorials/complex/01_**pdb2gmx.htmlhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/01_pdb2gmx.html tutorial But when i take complex structure directly from autodock result and run PDB2GMX it will give error because it is not recognizing ligand topology which is in complex structure. Then i followed justin tutorial took protein alone and applied Charmm27 Force field and used generate ligand topologies using Swissparam tool ( http://swissparam.ch/) when i do Editconf and created cubic box ligand is going away from protein. Actually my main task to place ligand in paraticular binding site in my protein and perform molecular dynamics. Can any body tell me how to do this..? Whatever you're doing is changing the coordinates that you originally had. You don't want to do that. -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/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- 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 -- Sainitin D PhD student Bioinformatics Group Biotechnology Center Technische Universität Dresden Tatzberg 47/49 01307 Dresden, Germany Tel Lab:+49 (0)351 463 40060 -- 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] Protein ligand molecular dynamics simulation
On 18/04/2012 6:58 AM, sai nitin wrote: Hi Justin, I generated topologies of my protein using PDB2GMX (charmm27 FF) and ligand topology using swissparam tool using Charmm force field i included ligand.itp file in topol.top of protein. And i used docked complex structure (protein + ligand) from docking analysis and generated boxed.pdb next i created solvated.pdb using (editconf and genbox tools) and also checked SOL molecules updated in topol.top file next i checked solvated.pdb file in pymol my ligand is in correct place in protein the way i wanted but problem came after this while using grompp I used grompp tool to minimize this solvated.pdb it is showing following error..using em.mdp Fatal Error number of coordinates in coordinate file (solvated.pdb, 51540) does not match topology (topol.top, 52756) I know this is commonly known issue for new users of gromacs. I looked up in gmx-archive list couldnt find optimal solution for my problem.. Let me know how to solve this ...issue... It means exactly what it says. Your coordinate file and topology must refer to the same system. See last para of manual 5.7.1. Mark Cheers, Nitin On Mon, Apr 16, 2012 at 5:03 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: sai nitin wrote: Hi all, I have done complex (protein + ligand) complex from autodock software using this complex im trying to follow http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/01_pdb2gmx.html tutorial But when i take complex structure directly from autodock result and run PDB2GMX it will give error because it is not recognizing ligand topology which is in complex structure. Then i followed justin tutorial took protein alone and applied Charmm27 Force field and used generate ligand topologies using Swissparam tool (http://swissparam.ch/) when i do Editconf and created cubic box ligand is going away from protein. Actually my main task to place ligand in paraticular binding site in my protein and perform molecular dynamics. Can any body tell me how to do this..? Whatever you're doing is changing the coordinates that you originally had. You don't want to do that. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing list gmx-users@gromacs.org mailto:gmx-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 mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Sainitin D PhD student Bioinformatics Group Biotechnology Center Technische Universität Dresden Tatzberg 47/49 01307 Dresden, Germany Tel Lab:+49 (0)351 463 40060 -- 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
[gmx-users] Protein ligand molecular dynamics simulation
Hi all, I have done complex (protein + ligand) complex from autodock software using this complex im trying to follow http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/01_pdb2gmx.html tutorial But when i take complex structure directly from autodock result and run PDB2GMX it will give error because it is not recognizing ligand topology which is in complex structure. Then i followed justin tutorial took protein alone and applied Charmm27 Force field and used generate ligand topologies using Swissparam tool ( http://swissparam.ch/) when i do Editconf and created cubic box ligand is going away from protein. Actually my main task to place ligand in paraticular binding site in my protein and perform molecular dynamics. Can any body tell me how to do this..? Thanks in advance -- Sainitin D -- 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] Protein ligand molecular dynamics simulation
On Mon, Apr 16, 2012 at 11:01 PM, sai nitin sainit...@gmail.com wrote: Hi all, I have done complex (protein + ligand) complex from autodock software using this complex im trying to follow http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/01_pdb2gmx.html tutorial But when i take complex structure directly from autodock result and run PDB2GMX it will give error because it is not recognizing ligand topology which is in complex structure. Then i followed justin tutorial took protein alone and applied Charmm27 Force field and used generate ligand topologies using Swissparam tool (http://swissparam.ch/) when i do Editconf and created cubic box ligand is going away from protein. Actually my main task to place ligand in paraticular binding site in my protein and perform molecular dynamics. Can any body tell me how to do this..? 1] pdb2gmx generate ligands.top (if possible, basically you need generate your ligand.itp by other ways) and rename it as ligands.itp 2] pdb2gmx generate protein.top and rename it as protein.itp (also need delete some entry) 3] create the topol.top includes the ligands.itp and protein.itp, take care the double entry. (To make it easy, you may take some pdb with several chains. use pdb2gmx and see how those top files combined together.) 4] The docked structure skip the pdb2gmx step. go directly to the editconf. You may do a try, but it will be helpful if you are a bit familiar with how to combine those top_files. Thanks in advance -- Sainitin D -- gmx-users mailing list gmx-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 -- 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
