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

[Justin A. Lemkul]

vinothkumar mohanakrishnan wrote:
> Dear Justin
> 
> what corrections i should make to ffoplsaan.itp to make it correct. what 
> i should give instead of CAB and CLAA?.
> 

You must use atom types, not names.  Unfortunately, you've chosen to use atom 
names, which are also types, which makes all of this quite confusing if you're 
not sure what you're doing.

You defined two new atom types - opls_966 (CAB) and opls_967 (CLAA), which are 
the only indicators you are allowed to use if introducing new types.  Thus, 
references to atom names (CAC, CLAD) will generate fatal errors.

> 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)?
> 

Your topology needs to be consistent with whatever files need to be included. 
By default, Gromacs checks the working directory first, but if you've moved to a 
new (sub)directory to carry out further steps, the grompp will not find your 
modified files, but will instead locate only the default force field files in 
$GMXLIB.  Either keep all your work in one directory (which can get messy), or 
make use of the "include" keyword in the .mdp file.  Any directory specified 
there will be searched after the working directory, but before $GMXLIB.

-Justin

> Regards
> Vinoth
> 
> On Mon, Oct 18, 2010 at 5:27 PM, Justin A. Lemkul <jalemkul at vt.edu 
> <mailto: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 <http://vt.edu> | (540) 231-9080
>     http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> 
>     ========================================
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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

========================================