[gmx-users] Grompp error : Incorrect number of parameters

Wed Dec 20 11:31:22 CET 2017

Hi,

The large energy means your topology is probably broken. Please use a tool
that will write an .itp file for you (e.g. SwissParam?), or next time get
your topology for your ligand working before you try to use it in a
complex. Even get a simple form of the ligand working first, to teach
yourself the process of writing the coordinate file. The more new things
you try to do at once, the less likely you are to fail in ways that you can
help yourself to fix.

Mark

On Wed, Dec 20, 2017 at 8:24 PM RAHUL SURESH <drrahulsuresh at gmail.com>
wrote:

> To be included here, the ligand I have uploaded seems to be so congested
> and out of form. Look literally like a clumsy ball.
> I am not sure what make this happen.
>
> On Wed, Dec 20, 2017 at 2:51 PM, RAHUL SURESH <drrahulsuresh at gmail.com>
> wrote:
>
> > Dear Alex
> >
> > I have tried that but the system collapse. For em_real.mdp option,I get
> > message stating
> >
> > Energy minimization has stopped, but the forces have not converged to the
> > requested precision Fmax < 1000 (which may not be possible for your
> > system).
> > It stopped because the algorithm tried to make a new step whose size was
> > too
> > small, or there was no change in the energy since last step. Either way,
> we
> > regard the minimization as converged to within the available machine
> > precision, given your starting configuration and EM parameters.
> >
> > Double precision normally gives you higher accuracy, but this is often
> not
> > needed for preparing to run molecular dynamics.
> > You might need to increase your constraint accuracy, or turn
> > off constraints altogether (set constraints = none in mdp file)
> >
> > writing lowest energy coordinates.
> >
> > Back Off! I just backed up em.gro to ./#em.gro.1#
> >
> > Steepest Descents converged to machine precision in 15 steps,
> > but did not reach the requested Fmax < 1000.
> > Potential Energy  =  3.9192084e+11
> > Maximum force     =  1.3457252e+14 on atom 629
> > Norm of force     =  1.0629695e+12
> >
> > Simulation ended prematurely, no performance report will be written.
> >
> > GROMACS reminds you: "When It Starts to Start It'll Never Stop"
> (Magnapop)
> >
> >
> > On Wed, Dec 20, 2017 at 2:20 PM, Alex <nedomacho at gmail.com> wrote:
> >
> >> The description for the Urey-Bradley potential (assuming two quadratic
> >> terms qualify for the proud term "potential") is described in the user
> >> manual, and the constants' order of appearance in the itp file is given
> in
> >> the Table 5.5 of the manual. If you have a basic quadratic angular term
> >> (first term in U-B with two constants) from elsewhere and you want to
> use
> >> it in the U-B format, it is an absolutely trivial task. All you have to
> do
> >> is set the U-B distance-dependent energy component to zero.
> >>
> >> Alex
> >>
> >>
> >>
> >> On 12/20/2017 12:05 AM, RAHUL SURESH wrote:
> >>
> >>> Hi
> >>>
> >>> Thank you Mark.
> >>>
> >>> On Wed, Dec 20, 2017 at 12:29 PM, Mark Abraham <
> mark.j.abraham at gmail.com
> >>> >
> >>> wrote:
> >>>
> >>> Hi,
> >>>>
> >>>> Sorry I don't know how any of these non-GROMACS tools work, or even
> >>>> whether
> >>>> they actually generate Urey Bradley interactions that have all the
> >>>> terms. I
> >>>> suggest you spend some time with the documentation.
> >>>>
> >>>> Mark
> >>>>
> >>>> On Wed, Dec 20, 2017, 5:15 PM RAHUL SURESH <drrahulsuresh at gmail.com>
> >>>> wrote:
> >>>>
> >>>> Sorry Mark, I failed to note that.
> >>>>>
> >>>>> I am afraid that I don't know what that are those components and how
> >>>>> and
> >>>>> where to find it. If you are actually meaning about "ub0 kub"
> >>>>>
> >>>> components,
> >>>>
> >>>>> how could i find the value for it. In case of swiss param generated
> itp
> >>>>> file, these components appear to be 0. Any help here please?
> >>>>>
> >>>>>
> >>>>> On Wed, Dec 20, 2017 at 10:19 AM, Mark Abraham <
> >>>>> mark.j.abraham at gmail.com
> >>>>>
> >>>>> wrote:
> >>>>>
> >>>>> Hi,
> >>>>>>
> >>>>>> Please read my answer.
> >>>>>>
> >>>>>> Mark
> >>>>>>
> >>>>>> On Wed, Dec 20, 2017, 3:43 PM RAHUL SURESH <drrahulsuresh at gmail.com
> >
> >>>>>> wrote:
> >>>>>>
> >>>>>> On Wed, 20 Dec 2017 at 5:06 AM, Justin Lemkul <jalemkul at vt.edu>
> >>>>>>>
> >>>>>> wrote:
> >>>>
> >>>>>
> >>>>>>>> On 12/19/17 11:14 AM, RAHUL SURESH wrote:
> >>>>>>>>
> >>>>>>>>> Dear all
> >>>>>>>>>
> >>>>>>>>> For grompp em.mdp I get an error
> >>>>>>>>>
> >>>>>>>>> ERROR 1 [file THC.itp, line 89]:
> >>>>>>>>>     Incorrect number of parameters - found 2, expected 4 or 8 for
> >>>>>>>>>
> >>>>>>>> U-B.
> >>>>>
> >>>>>> My itp file as follows
> >>>>>>>>>
> >>>>>>>>> [ angles ]
> >>>>>>>>>
> >>>>>>>>> 1   2   29   5    79.178   109.588     *{Line 89}*
> >>>>>>>>> 1   2   3     5    32.192   112.817
> >>>>>>>>> 2   3   31   5    51.424   109.189
> >>>>>>>>>
> >>>>>>>>>   From the manual chapter 5, function of U-B is 5. And it works
> >>>>>>>>>
> >>>>>>>> fine
> >>>>
> >>>>> for
> >>>>>>
> >>>>>>> function type 2 and 8.
> >>>>>>>>>
> >>>>>>>>> Any thing better could be done?
> >>>>>>>>>
> >>>>>>>> As the error tells you, the U-B functional form requires at least
> 4
> >>>>>>>> parameters; look at its functional form. See Table 5.5.
> >>>>>>>>
> >>>>>>>
> >>>>>>> Dear Justin
> >>>>>>>
> >>>>>>> But the parameter obtained from ffTK have only two. What could be
> >>>>>>>
> >>>>>> done.?
> >>>>>
> >>>>>>
> >>>>>>>> -Justin
> >>>>>>>>
> >>>>>>>> --
> >>>>>>>> ==================================================
> >>>>>>>>
> >>>>>>>> Justin A. Lemkul, Ph.D.
> >>>>>>>> Assistant Professor
> >>>>>>>> Virginia Tech Department of Biochemistry
> >>>>>>>>
> >>>>>>>> 303 Engel Hall
> >>>>>>>> 340 West Campus Dr.
> >>>>>>>> Blacksburg, VA 24061
> >>>>>>>>
> >>>>>>>> jalemkul at vt.edu | (540) 231-3129
> >>>>>>>> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
> >>>>>>>>
> >>>>>>>> ==================================================
> >>>>>>>>
> >>>>>>>> --
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> >>>>>>>> --
> >>>>>>> *Regards,*
> >>>>>>> *Rahul Suresh*
> >>>>>>> *Research Scholar*
> >>>>>>> *Bharathiar University*
> >>>>>>> *Coimbatore*
> >>>>>>> --
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> >>>>>
> >>>>> --
> >>>>> *Regards,*
> >>>>> *Rahul Suresh*
> >>>>> *Research Scholar*
> >>>>> *Bharathiar University*
> >>>>> *Coimbatore*
> >>>>> --
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> >
> >
> >
> > --
> > *Regards,*
> > *Rahul Suresh*
> > *Research Scholar*
> > *Bharathiar University*
> > *Coimbatore*
> >
>
>
>
> --
> *Regards,*
> *Rahul Suresh*
> *Research Scholar*
> *Bharathiar University*
> *Coimbatore*
> --
> Gromacs Users mailing list
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