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

[Justin A. Lemkul]

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
> 

-- 
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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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