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

[Alex]

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
>>>>>>
>>>>>> ==================================================
>>>>>>
>>>>>> --
>>>>>> Gromacs Users mailing list
>>>>>>
>>>>>> * Please search the archive at
>>>>>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>>>>>> posting!
>>>>>>
>>>>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>>>>
>>>>>> * For (un)subscribe requests visit
>>>>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
>>> or
>>>>>> send a mail to gmx-users-request at gromacs.org.
>>>>>>
>>>>> --
>>>>> *Regards,*
>>>>> *Rahul Suresh*
>>>>> *Research Scholar*
>>>>> *Bharathiar University*
>>>>> *Coimbatore*
>>>>> --
>>>>> Gromacs Users mailing list
>>>>>
>>>>> * Please search the archive at
>>>>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>>>>> posting!
>>>>>
>>>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>>>
>>>>> * For (un)subscribe requests visit
>>>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
>> or
>>>>> send a mail to gmx-users-request at gromacs.org.
>>>>>
>>>> --
>>>> Gromacs Users mailing list
>>>>
>>>> * Please search the archive at http://www.gromacs.org/
>>>> Support/Mailing_Lists/GMX-Users_List before posting!
>>>>
>>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>>
>>>> * For (un)subscribe requests visit
>>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>>>> send a mail to gmx-users-request at gromacs.org.
>>>>
>>>
>>>
>>> --
>>> *Regards,*
>>> *Rahul Suresh*
>>> *Research Scholar*
>>> *Bharathiar University*
>>> *Coimbatore*
>>> --
>>> Gromacs Users mailing list
>>>
>>> * Please search the archive at
>>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>>> posting!
>>>
>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>
>>> * For (un)subscribe requests visit
>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>>> send a mail to gmx-users-request at gromacs.org.
>>>
>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at http://www.gromacs.org/
>> Support/Mailing_Lists/GMX-Users_List before posting!
>>
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>> * For (un)subscribe requests visit
>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>> send a mail to gmx-users-request at gromacs.org.
>>
>
>