[gmx-users] GROMACS/ORCA QMMM
swati patel
swatipatel088 at gmail.com
Thu Nov 17 22:07:49 CET 2011
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 <jrta1981 at 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 <jalemkul at 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 <jalemkul at 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 at gromacs.org
> >>> http://lists.gromacs.org/mailman/listinfo/gmx-users
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> >>>
> >>
> >
> > --
> > ========================================
> >
> > 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 at gromacs.org
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