[gmx-users] Reg: Running Energy minimisation for dichloroethane (DCE)

[Mark Abraham]

  On 18/10/2010 10:31 PM, vinothkumar mohanakrishnan wrote:
> Hi all
>
> i added new atomtype for dichloroethane (DCE) and added the 
> corresponding parameters in the .rtp, .atp, .bon.itp, .nb.itp 
> respectively. given below are my additions to the corresponding files 
> respectively.
>
> *ffoplsaa.rtp*
>
> [ DCE ]
>  [ atoms ]
>  CLAA opls_967 -0.2270  1
>  CAB  opls_966  0.2270  1
>  CAC  opls_966  0.2270  2
>  CLAD opls_967 -0.2270  2
>
> [ bonds ]
>  CLAA    CAB
>  CAB    CAC
>  CAC    CLAD
>
> [ angles ]
>  CLAA    CAB    CAC
>  CAB    CAC    CLAD
>
> [ dihedrals ]
>  CLAA    CAB    CAC    CLAD
>
> *ffoplsaa.atp*
>
>  opls_966   14.02700  ; CH2 for DCE
>  opls_967   35.45300  ; CL for DCE
>
> *ffoplsaabon.itp*
>
> [bondtypes]
> CLAA  CAB     1    0.17870   194137.6   ; CL-CH2 for DCE
> CAB   CAC     1    0.15300   259408.0   ; CH2-CH2 for DCE
> CAC   CLAD    1    0.17870   194137.6   ; CL-CH2 for DCE
>
> [angletypes]
> CLAA  CAB   CAC       1   108.200    368.192   ; C-C-CL for DCE
> CAB   CAC   CLAD      1   108.200    368.192   ; C-C-CL for DCE
>
> [dihedraltypes]
> CLAA   CAB     CAC   CLAD     3     20.76096  -0.4184   27.011904  
> 0.00000   0.00000   0.00000 ; for DCE
>
> *ffoplsaanb.itp*
>
> opls_966   CAB    6    14.02700    0.227       A    3.98000e-01  
> 4.76976e-01 ; CH2 of DCE
> opls_967   CLAA   17   35.45300   -0.227       A    3.16000e-01  
> 0.20920e+01 ; Cl of DCE
>
> *dce.pdb*
>
> HETATM    1 CLAA DCE     1       6.300  -2.280   1.360  1.00 
> 20.00            CL
> HETATM    2  CAB DCE     1       5.060  -3.540   1.500  1.00 
> 20.00             C
> HETATM    3  CAC DCE     1       4.320  -3.740   0.170  1.00 
> 20.00             C
> HETATM    4 CLAD DCE     1       3.270  -2.350  -0.210  1.00 
> 20.00            CL
>
> After adding all this, when i run grompp i get the error as *fatal 
> error Unknown bond_atomtype CLAA*. can any one tell me why this happens?.

I can't tell until I know how you've invoked grompp, and how you 
generated the .top file it needs, and which line of that .top grompp 
doesn't like. When asking for help, please copy and paste all your 
relevant commands, and any error messages in full, and any relevant 
chunk of the .top. Check whether that .top file is #including the 
correct .itp files.

Mark
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