Hi Justin, I tried using a larger step size but my system blew up... My guess is that I have a bad starting structure, I'll work on the initial structure for the QM region (energy minimize).
When I'm running ORCA I want to have a LJ file to correct for the interaction of my QM system with the protein. However this file is not created when I run QMMM, I've used the bOpt = true in the mdp file. Can anyone please offer some help on how to create this LJ files? Thanks, Jose Tusell On Thu, Nov 17, 2011 at 2:07 PM, swati patel <swatipatel...@gmail.com> wrote: > hello, > I am trying to simulate streptavidin tetramer-biotin complex.I ve calculated > Ligand topology from a sofware PRODRG using gromos87 force fields.After > solvating it,I am getting an error using grompp command > > Fatal error: > Atomtype HW not found > > can anyone provide me some help? > > Thanx with anticipation. > > > On Fri, Nov 18, 2011 at 2:29 AM, Jose Tusell <jrta1...@gmail.com> wrote: >> >> I'll try changing the step size first and if that fails I'll try >> another algorithm. Thanks for the input. >> >> Jose Tusell >> >> On Thu, Nov 17, 2011 at 11:48 AM, Justin A. Lemkul <jalem...@vt.edu> >> wrote: >> > >> > >> > Jose Tusell wrote: >> >> >> >> Hi Justin, >> >> >> >> Thanks for the input on why this is happening. It sounds a little >> >> suspicious that the energy doesn't change after a few steps of energy >> >> minimization. Do you know of any way that I can find out what is >> >> going on? >> >> >> > >> > The screen output should indicate the atom with maximal force. >> > Sometimes >> > the EM algorithms get stuck when the geometry cannot change without >> > making >> > detrimental moves. You either need a larger step size, a different >> > algorithm, or a better starting structure, if that is the case. I have >> > seen >> > this many times before, nothing suspicious about it. >> > >> > -Justin >> > >> >> Thanks, >> >> >> >> Jose Tusell >> >> >> >> On Thu, Nov 17, 2011 at 10:58 AM, Justin A. Lemkul <jalem...@vt.edu> >> >> wrote: >> >>> >> >>> Jose Tusell wrote: >> >>>> >> >>>> Hi Cristoph, >> >>>> >> >>>> Thanks for the reply. I found that my problem was not gromacs. The >> >>>> input that ORCA was receiving from GROMACS did not have the correct >> >>>> number of hydrogens. I've solved this problem now and ORCA is >> >>>> running >> >>>> fine. I however ran into another problem with my energy >> >>>> minimization. >> >>>> The output from my gromacs log file is the following: >> >>>> >> >>>> Step Time Lambda >> >>>> 0 0.00000 0.00000 >> >>>> >> >>>> Energies (kJ/mol) >> >>>> Bond Angle Proper Dih. Improper Dih. >> >>>> LJ-14 >> >>>> 1.21899e+04 1.92496e+03 5.62567e+03 1.49141e+01 >> >>>> 3.68001e+03 >> >>>> Coulomb-14 LJ (SR) Coulomb (SR) Coul. recip. Quantum >> >>>> En. >> >>>> 2.41200e+04 1.47494e+05 -5.06544e+05 -7.56009e+04 >> >>>> -3.96508e+06 >> >>>> Potential Pressure (bar) >> >>>> -4.35218e+06 -2.10629e+04 >> >>>> >> >>>> Step Time Lambda >> >>>> 1 1.00000 0.00000 >> >>>> >> >>>> Energies (kJ/mol) >> >>>> Bond Angle Proper Dih. Improper Dih. >> >>>> LJ-14 >> >>>> 1.20006e+04 1.92297e+03 5.62600e+03 1.47801e+01 >> >>>> 3.67746e+03 >> >>>> Coulomb-14 LJ (SR) Coulomb (SR) Coul. recip. Quantum >> >>>> En. >> >>>> 2.41174e+04 1.46421e+05 -5.06609e+05 -7.56156e+04 >> >>>> -4.00402e+06 >> >>>> Potential Pressure (bar) >> >>>> -4.39246e+06 -2.10739e+04 >> >>>> >> >>>> Step Time Lambda >> >>>> 2 2.00000 0.00000 >> >>>> >> >>>> Energies (kJ/mol) >> >>>> Bond Angle Proper Dih. Improper Dih. >> >>>> LJ-14 >> >>>> 1.17961e+04 1.92126e+03 5.62633e+03 1.46477e+01 >> >>>> 3.67461e+03 >> >>>> Coulomb-14 LJ (SR) Coulomb (SR) Coul. recip. Quantum >> >>>> En. >> >>>> 2.41145e+04 1.45528e+05 -5.06679e+05 -7.56315e+04 >> >>>> -4.18671e+06 >> >>>> Potential Pressure (bar) >> >>>> -4.57635e+06 -2.10854e+04 >> >>>> >> >>>> Step Time Lambda >> >>>> 3 3.00000 0.00000 >> >>>> >> >>>> Step Time Lambda >> >>>> 4 4.00000 0.00000 >> >>>> >> >>>> Energies (kJ/mol) >> >>>> Bond Angle Proper Dih. Improper Dih. >> >>>> LJ-14 >> >>>> 1.16705e+04 1.92041e+03 5.62652e+03 1.45728e+01 >> >>>> 3.67282e+03 >> >>>> Coulomb-14 LJ (SR) Coulomb (SR) Coul. recip. Quantum >> >>>> En. >> >>>> 2.41128e+04 1.45113e+05 -5.06721e+05 -7.56410e+04 >> >>>> -4.24486e+06 >> >>>> Potential Pressure (bar) >> >>>> -4.63509e+06 -2.10913e+04 >> >>>> >> >>>> Step Time Lambda >> >>>> 5 5.00000 0.00000 >> >>>> >> >>>> Step Time Lambda >> >>>> 6 6.00000 0.00000 >> >>>> >> >>>> Step Time Lambda >> >>>> 7 7.00000 0.00000 >> >>>> >> >>>> Step Time Lambda >> >>>> 8 8.00000 0.00000 >> >>>> >> >>>> Step Time Lambda >> >>>> 9 9.00000 0.00000 >> >>>> >> >>>> Step Time Lambda >> >>>> 10 10.00000 0.00000 >> >>>> >> >>>> Step Time Lambda >> >>>> 11 11.00000 0.00000 >> >>>> >> >>>> Step Time Lambda >> >>>> 12 12.00000 0.00000 >> >>>> >> >>>> Step Time Lambda >> >>>> 13 13.00000 0.00000 >> >>>> >> >>>> Step Time Lambda >> >>>> 14 14.00000 0.00000 >> >>>> >> >>>> Step Time Lambda >> >>>> 15 15.00000 0.00000 >> >>>> >> >>>> Step Time Lambda >> >>>> 16 16.00000 0.00000 >> >>>> >> >>>> Step Time Lambda >> >>>> 17 17.00000 0.00000 >> >>>> >> >>>> Step Time Lambda >> >>>> 18 18.00000 0.00000 >> >>>> >> >>>> >> >>>> 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. >> >>>> You might need to increase your constraint accuracy, or turn >> >>>> off constraints alltogether (set constraints = none in mdp file) >> >>>> >> >>>> Why doesn't GROMACS output the energies for certain steps? Step 3 >> >>>> and >> >>>> steps 5-18 do show any output in the log file. Any ideas why this is >> >>>> happening? >> >>>> >> >>> This happens for the reasons printed by mdrun - those steps caused no >> >>> change >> >>> in energy. >> >>> >> >>> -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 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 >> >>> >> >> >> > >> > -- >> > ======================================== >> > >> > 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 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 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 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 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
