[gmx-users] No default Ryckaert-Bell. types

[Justin Lemkul]

On 8/14/18 4:16 AM, Baolin Huang wrote:
> Hi Dan and all guys,
> Thanks for your answers. I find that the OPLS-AA force field does not contain the dihedral force-field parameters of the Chain_C. Actually, my Chain_C was a hydroxyapatite (HAP, inorganic material) model. I also notice that the bond types of HAP in the ffbonded.itp file are missing.
> Following are some parameters from my ffbonded.itp file.
> [ dihedraltypes ]
> ;  i    j    k    l   func     coefficients
> C3     CT     NT     C3      3      1.78866   3.49154   0.53555  -5.81576   0.00000   0.00000 ; (From wildcard) amine all-atom
> [ bondtypes ]
> ; i    j  func       b0          kb
>    OW    HW      1    0.09572   502080.0   ; For TIP4F Water - wlj 1/98
>   
> My question is that what are the meanings of the i, j, k, l, func, coefficients, b0, and kb? How to find the values of those of HAP? Just list some [bonds] and [dihedrals] of my Chain_C as follows.

Start with the manual, where all file formats are explained.

You won't necessarily "find" the values to plug in here unless someone 
has already published them. You may need to do the force field 
parametrization yourself.

-Justin

> [ bonds ]
>   O1  P27
>   O10 P27
>   O13 P27
>   O14 P27
>   O2  P28
> [ dihedrals ]
>      O1    P27   O10  O13
>      O1    P27   O10  O14
>      O1    P27   O13  O10
>      O1    P27   O13  O14
>      O1    P27   O14  O13
>   
> Thanks for your time and any suggestions.
> Kind regards,
> Baolin
>   
>   
>   
>   
>   
> ------------------ Original ------------------
> From:  "Dan Gil"<dan.gil9973 at gmail.com>;
> Date:  Tue, Aug 14, 2018 04:39 AM
> To:  "gmx-users"<gmx-users at gromacs.org>;
>
> Subject:  Re: [gmx-users] No default Ryckaert-Bell. types
>
>   
> Hello,
>
> This is telling you that the OPLS-AA force field does not have the dihedral
> force-field parameters for your molecule (topol_Other_chain_C.itp) of the
> Ryckaert-Bell type. Your exact problem might be:
> (1) There is something wrong with the molecule topology.
> (2) OPLS-AA really doesn't have the dihedral force-field parameters, and
> you need to use another force-field.
>
> If your molecule is a simple hydrocarbon, it is unlikely that OPLS-AA has
> missing parameters.
>
> Dan
>
> On Sat, Aug 11, 2018 at 10:52 AM, Baolin Huang <hblin at gzhu.edu.cn> wrote:
>
>> Dear All,
>>    I experienced an error as follows: (I used the OPLS-AA force field)
>>    ERROR 48600 [file topol_Other_chain_C.itp, line 144934]:
>>    No default Ryckaert-Bell. types
>>
>>
>> Anyone can help?
>> Kind regards,
>>
>>
>> ------------------
>>
>> Dr. Baolin Huang
>> Lecturer, School of Life Sciences, Guangzhou University
>> --
>> 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.
>>

-- 
==================================================

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.thelemkullab.com

==================================================