[gmx-users] No default Ryckaert-Bell. types
jalemkul at vt.edu
Wed Aug 15 13:28:50 CEST 2018
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
> [ 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,
> ------------------ 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
> 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.
> 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
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Justin A. Lemkul, Ph.D.
Virginia Tech Department of Biochemistry
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