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

[Justin Lemkul]

On 6/6/13 11:52 AM, Nilesh Dhumal wrote:
> I checked the line number in .top file. Its not reading any dihedral
> parameter defined in .itp file.
>

Well, if it's not reading parameters, then that explains the error that tells 
you there are no parameters defined.

-Justin

>> 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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>

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

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

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