[gmx-users] : Incorrect number of parameters - found 4, expected 6 or 12.

Florian Dommert dommert at fias.uni-frankfurt.de
Wed Sep 10 12:17:06 CEST 2008


* Justin A. Lemkul <jalemkul at vt.edu> [2008-09-10 05:46:07 -0400]:

>
>
> Morteza Khabiri wrote:
>> Dear justin,
>> I have made the itp file on a basis of chapter 5 of gromacs. Every things
>> seems fine. my itp file for opls is as follow:
>
> "Seems fine" is your own evaluation, but if grompp is giving you errors 
> about an incorrect topology, then indeed it is not.  Did grompp tell you a 
> line number that caused the error?  My guess would be yes.  If you want free 
> help for solving this, you have to make it easy.  What was the line?  What 
> is on that line?
>
> -Justin
>
>> ;
>> [ moleculetype ]
>> ; Name nrexcl
>> DRG      3
>> [ atoms ]
>> ;   nr      type  resnr resid  atom  cgnr   charge     mass
>>      1   opls_185   1  DRG     HAD     1    0.02734   1.0080
>>      2   opls_182   1  DRG     CAL     1    0.10638  12.0110
>>      3   opls_185   1  DRG     HAE     1    0.02734   1.0080
>>      4   opls_180   1  DRG     OAI     1   -0.36111  15.9994
>>      5   opls_182   1  DRG     CAK     1    0.10638  12.0110
>>      6   opls_185   1  DRG     HAB     2    0.02734   1.0080
>>      7   opls_185   1  DRG     HAG     2    0.02734   1.0080
>>      8   opls_711   1  DRG     CAM     2    0.00235  12.0110
>>      9   opls_777   1  DRG     HAF     3    0.00857   1.0080
>>     10   opls_777   1  DRG     HAH     3    0.00857   1.0080
>>     11   opls_711   1  DRG     CAJ     3    0.00235  12.0110
>>     12   opls_777   1  DRG     HAC     3    0.00857   1.0080
>>     13   opls_777   1  DRG     HAA     3    0.00857   1.0080
>> [ bonds ]
>> ; ai  aj  fu    c0, c1, ...
>>    1   2   1    0.109    284512.0    0.109    284512.0 ;   HAD  CAL
>>    2   3   1    0.109    284512.0    0.109    284512.0 ;   CAL  HAE
>>    2   4   1    0.141    267776.0    0.141    267776.0 ;   CAL  HAI
>>    2  11   1    0.152    217568.0    0.152    217568.0 ;   CAL  CAJ
>>    4   5   1    0.141    267776.0    0.141    267776.0 ;   OAI  CAK
>>    5   6   1    0.109    284512.0    0.109    284512.0 ;   CAK  HAB
>>    5   7   1    0.109    284512.0    0.109    284512.0 ;   CAK  HAG
>>    5   8   1    0.151    234304.0    0.151    234304.0 ;   CAK  CAM
>>    8   9   1    0.108    284512.0    0.108    284512.0 ;   CAM  HAF
>>    8  10   1    0.108    284512.0    0.108    284512.0 ;   CAM  HAH
>>    8  11   1    0.150    217568.0    0.150    217568.0 ;   CAM  CAJ
>>   11  12   1    0.108    284512.0    0.108    284512.0 ;   CAJ  HAC
>>   11  13   1    0.108    284512.0    0.108    284512.0 ;   CAJ  HAA
>> [ pairs ]
>> ; ai  aj  fu    c0, c1, ...
>>    1   5   1                                           ;   HAD  CAK
>>    1   8   1                                           ;   HAD  CAM
>>    1  12   1                                           ;   HAD  HAC
>>    1  13   1                                           ;   HAD  HAA
>>    2   6   1                                           ;   CAL  HAB
>>    2   7   1                                           ;   CAL  HAG
>>    2   9   1                                           ;   CAL  HAF
>>    2  10   1                                           ;   CAL  HAH
>>    3   5   1                                           ;   HAE  CAK
>>    3   8   1                                           ;   HAE  CAM
>>    3  12   1                                           ;   HAE  HAC
>>    3  13   1                                           ;   HAE  HAA
>>    4   9   1                                           ;   OAI  HAF
>>    4  10   1                                           ;   OAI  HAH
>>    4  12   1                                           ;   OAI  HAC
>>    4  13   1                                           ;   OAI  HAA
>>    5  12   1                                           ;   CAK  HAC
>>    5  13   1                                           ;   CAK  HAA
>>    6   9   1                                           ;   HAB  HAF
>>    6  10   1                                           ;   HAB  HAH
>>      6   9   1                                           ;   HAB  HAF
>>    6  10   1                                           ;   HAB  HAH
>>    6  11   1                                           ;   HAB  CAJ
>>    7   9   1                                           ;   HAG  HAF
>>    7  10   1                                           ;   HAG  HAH
>>    7  11   1                                           ;   HAG  CAJ
>>    9  12   1                                           ;   HAF  HAC
>>    9  13   1                                           ;   HAF  HAA
>>   10  12   1                                           ;   HAH  HAC
>>   10  13   1                                           ;   HAH  HAA
>> [ angles ]
>> ; ai  aj  ak  fu    c0, c1, ...
>>    1   2   3   1    107.8       276.1    107.8       276.1 ;   HAD  CAL  
>> HAE
>>    1   2   4   1    109.5       292.8    109.5       292.8 ;   HAD  CAL  
>> OAI

Hello;

   the bond angles seem to be respondsible. You use function type 1. That
   means you just have a harmonic potential. To this end gromacs wants an
   equilibrium angle and a "spring constant". You provide 4 numbers. I
   dont the funtions in mind. However for function 1, it shoudl probably
   look like :

      1   2  11   1    110.7       313.8    ;   HAD  CAL  

However I do not which kind of function you want to chose. All this
information is given in Chapter 5 Topologies. Together with the
information about the calculation of bonded and nondbonded energy terms
you can set up the itp file correctly without any trouble.

Best Regards,

Flo

>> CAJ
>>    3   2   4   1    109.5       292.8    109.5       292.8 ;   HAE  CAL  
>> OAI
>>    3   2  11   1    110.7       313.8    110.7       313.8 ;   HAE  CAL  
>> CAJ
>>    4   2  11   1    109.5       292.8    109.5       292.8 ;   OAI  CAL  
>> CAJ
>>    2   4   5   1    109.5       502.0    109.5       502.0 ;   CAL  OAI  
>> CAK
>>    4   5   6   1    109.5       292.8    109.5       292.8 ;   OAI  CAK  
>> HAB
>>    4   5   7   1    109.5       292.8    109.5       292.8 ;   OAI  CAK  
>> HAG
>>    4   5   8   1    109.5       292.8    109.5       292.8 ;   OAI  CAK  
>> CAM
>>    6   5   7   1    107.8       276.1    107.8       276.1 ;   HAB  CAK  
>> HAG
>>    6   5   8   1    110.7       313.8    110.7       313.8 ;   HAB  CAK  
>> CAM
>>    7   5   8   1    110.7       313.8    110.7       313.8 ;   HAG  CAK  
>> CAM
>>    5   8   9   1    114.3       292.8    114.3       292.8 ;   CAK  CAM  
>> HAF
>>    5   8  10   1    114.3       292.8    114.3       292.8 ;   CAK  CAM  
>> HAH
>>    5   8  11   1    117.2       313.8    117.2       313.8 ;   CAK  CAM  
>> CAJ
>>    9   8  10   1    114.3       292.8    114.3       292.8 ;   HAF  CAM  
>> HAH
>>    9   8  11   1    117.2       313.8    117.2       313.8 ;   HAF  CAM  
>> CAJ
>>   10   8  11   1    117.2       313.8    117.2       313.8 ;   HAH  CAM  
>> CAJ
>>    2  11   8   1    117.2       313.8    117.2       313.8 ;   CAL  CAJ  
>> CAM
>>    2  11  12   1    114.3       292.8    114.3       292.8 ;   CAL  CAJ  
>> HAC
>>    2  11  13   1    114.3       292.8    114.3       292.8 ;   CAL  CAJ  
>> HAA
>>    8  11  12   1    117.2       313.8    117.2       313.8 ;   CAM  CAJ  
>> HAC
>>    8  11  13   1    117.2       313.8    117.2       313.8 ;   CAM  CAJ  
>> HAA
>>   12  11  13   1    114.3       292.8    114.3       292.8 ;   HAC  CAJ  
>> HAA
>> [ dihedrals ]
>> ; ai  aj  ak  al  fu    c0, c1, m, ...
>>    2   1   3   4   3     1.58  4.769       1.58  4.769   ; imp   CAL  HAD 
>> HAE  OAI
>>    5   4   6   7   3     1.58  4.769       1.58  4.769   ; imp   CAK  OAI 
>> HAB  HAG
>>    8   5  10   9   3     0.62  1.882       0.62  1.882   ; imp   CAM  CAK 
>> HAH  HAF
>>   11   2  12   8   3     0.62  1.882       0.62  1.882   ; imp   CAJ  CAL 
>> HAC  CAM
>>    1   2   4   5   3      1.5    4.7 3      1.5    4.7 3 ; dih   HAD  CAL 
>> OAI  CAK
>>   13  11   2   1   3      1.5    4.7 3      1.5    4.7 3 ; dih   HAA  CAJ 
>> CAL  HAD
>>    2   4   5   8   3      1.5    4.7 3      1.5    4.7 3 ; dih   CAL  OAI 
>> CAK  CAM
>>   11   8   5   4   3      1.5    4.7 3      1.5    4.7 3 ; dih   CAJ  CAM 
>> CAK  OAI
>>   13  11   8   5   3      0.6    1.8 3      0.6    1.8 3 ; dih   HAA  CAJ 
>> CAM  CAK
>> and I really could not find which parameter should I included.
>> Thanks
>> yours,
>> Morteza
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>
> -- 
> ========================================
>
> Justin A. Lemkul
> Graduate Research Assistant
> 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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-- 
Florian Dommert
Dipl.-Phys.

Computational and Theoretical Softmatter & Biophysics group

Frankfurt Institute for Advanced Studies
Johann-Wolfgang-Goethe University

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