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

RAHUL SURESH drrahulsuresh at gmail.com
Wed Dec 20 10:24:01 CET 2017 

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*

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