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

[Nilesh Dhumal]

I checked the line number in .top file. Its not reading any dihedral
parameter defined in .itp file.

NIlesh
>
> On 6/6/13 9:22 AM, Nilesh Dhumal wrote:
>> Hello,
>>
>> I am getting "No default Ryckaert-Bell. types" error for grompp.
>>
>> I have define all this parameter in  .itp file
>>
>> Here is .itp file
>>
>> ; For parameters see J. Phys. Chem. A. 2002, 106, 1074-1080
>> ; Derived from parsing of runfiles/alat.top.orig
>> ;[ defaults ]
>> ; nbfunc        comb-rule       gen-pairs       fudgeLJ fudgeQQ
>> ;1               3               yes             0.5     0.5
>> ; comb-rule 3 is square-root sigma, the OPLSAA version
>>
>> [ atomtypes ]
>> ; full atom descriptions are available in ffoplsaa.atp
>> ; name  bond_type    mass    charge   ptype          sigma      epsilon
>>   opls_124   S   16    32.06000     0.312       A    3.56000e-01
>> 1.65268e+00 opls_125   O   8     15.99940    -0.556       A
>> 2.93000e-01  1.17152e+00 opls_126   CT  6     15.03500    -0.148       A
>>    3.81000e-01  6.69440e-01 opls_140   HC  1      1.00800     0.090
>> A    2.50000e-01  1.25520e-01
>>
>>
>> [ bondtypes ]
>> ; i    j  func       b0          kb
>> S     O       1    0.1530   225936.0
>> S     CT      1    0.1800   100416.0
>> CT    HC      1    0.1110   134724.8
>>
>>
>> [ angletypes ]
>> ;  i    j    k  func       th0       cth
>>    CT     S      CT      1    95.0      142.256
>>    CT     S      O       1   106.75     330.536
>>    S      CT     HC      1   111.3      192.8824
>>    HC     CT     HC      1   108.4      148.532
>>
>>
>> [ dihedraltypes ]
>> ;  i    j    k    l   func     coefficients
>> ; OPLS Fourier dihedraltypes translated to Gromacs Ryckaert-Bellemans
>> form
>> ; according to the formula in the Gromacs manual.
>> CT     S      CT     HC      3      1.35352   4.06057   0.00000
>> -5.41410
>>   0.00000   0.00000 ; sulfide all-atom
>>   O     S     CT      HC      3      0.00000   0.00000   0.00000
>> 0.00000
>> 0.00000   0.00000 ; small ring
>>
>>
>>
>> Why I am getting this error.
>>
>
> Apparently grompp is failing to find some needed parameter.  You should
> get a
> line number in the topology where this is occurring, which will allow you
> to map
> back the atoms involved.
>
> -Justin
>
> --
> ========================================
>
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
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