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 <[email protected]> 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<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 | (540) 231-9080 > http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin> > > ==============================**========== > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> > Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<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 [email protected]. > Can't post? Read > http://www.gromacs.org/**Support/Mailing_Lists<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
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