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 >
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