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

[vinothkumar mohanakrishnan]

Dear Justin

what corrections i should make to ffoplsaan.itp to make it correct. what i
should give instead of CAB and CLAA?.

i copied the .rtp .atp .itp files from usr/local/gromacs/share/gromacs/top
to my working directory and added these parameters to the corresponding
files. what you mean is should i need to add these parameters to the source
directory ( usr/local/gromacs/share/gromacs/top)?

Regards
Vinoth

On Mon, Oct 18, 2010 at 5:27 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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
>>
>>
> You shouldn't be using atom names in the [*types] directives.  What you
> should be using are the interpolated types from ffoplsaanb.itp, thus you
> have only utilized opls_966 (CAB) and opls_967 (CLAA).
>
>  *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?.
>>
>>
> Have you been sure to #include the correct (modified) force field files?
>  That is, if you made a local copy and adjusted them, these won't be the
> files that pdb2gmx will #include by default.
>
> -Justin
>
>  Regards
>> Vinoth
>>
>>
> --
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> 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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