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

[Justin Lemkul]

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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