Thanks Justin, I must inform you that my pdb file has a modified cysteine residue having a mercury atom attached to the sulphur atom next to the residue having the atom 2700. Is the murcury atom creating any problem? I want to also know can I use amber forcefield in GROMACS for pdb files of lipid?
On Tue, Nov 8, 2011 at 5:56 PM, Justin A. Lemkul <jalem...@vt.edu> wrote: > > > madhumita das wrote: > >> >> Hi GROMACS users, >> >> i am in the midst of simulating a protein in water. I have modified >> a residue in my pdb file at position 182, using amber and then >> acpype.py. But after running the energy minimization step,using em.mdp >> file generated from acpype , following error comes. >> >> Steepest Descents: >> Tolerance (Fmax) = 1.00000e+03 >> Number of steps = 5000 >> Step= 17, Dmax= 1.5e-06 nm, Epot= 9.89827e+17 Fmax= inf, atom= >> 2700 >> Stepsize too small, or no change in energy. >> Converged to machine precision, >> but not to the requested precision Fmax < 1000 >> >> Double precision normally gives you higher accuracy. >> >> writing lowest energy coordinates. >> >> Steepest Descents converged to machine precision in 18 steps, >> but did not reach the requested Fmax < 1000. >> Potential Energy = 9.8982703e+17 >> Maximum force = inf on atom 2700 >> Norm of force = 1.7474532e+19 >> > > An infinite force suggests severe atomic overlap. Check the starting > structure, paying close attention to atom 2700 and its surrounding > environment. > > -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 gmx-users@gromacs.org > 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 gmx-users-requ...@gromacs.org. > Can't post? Read > http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> >
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