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

[vinothkumar mohanakrishnan]

Dear Mark

I generated the topology using pdb2gmx using dce.pdb. i checked the .top
file and i contains necessary .itp files. the error message that i get is
given below. any help is highly appreciated.

Program grompp, VERSION 4.0.7
Source code file: toppush.c, line: 620

Fatal error:
Unknown bond_atomtype CLAA

Regards
Vinoth


On Mon, Oct 18, 2010 at 5:12 PM, Mark Abraham <Mark.Abraham at anu.edu.au>wrote:

>  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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