[gmx-users] Overriding atom type.

[Justin Lemkul]

On 12/4/19 6:32 AM, Yogesh Sharma wrote:
> Thank you Dr. Alessandra
>
> I actually generated topologies for my ligands  using charmm server
>
> generated itp files had few overriding names, which are throwing errors
> when combined.

You can't introduce duplicate parameters. If you have multiple ligands 
that make use of the same paramters, the directive [atomtypes], 
[bondtypes], etc. must be merged into a single .itp file and #included.

I will note that these atom types are already standard in our CHARMM36 
port (including CGenFF) for GROMACS. I don't know which server you used 
but these should not be new atom types.

-Justin

> Please have a look at the itp files pasted here.
> ...........................................................................................................................
> [ atomtypes ]
> ; name at.num mass charge ptype sigma epsilon ; sigma_14 epsilon_14
>     CG2O6     6    12.0110      0.600     A    3.56359487256e-01
>   2.928800e-01
>      HGP1     1     1.0080      0.340     A    4.00013524445e-02
>   1.924640e-01
>     NG2S2     7    14.0070     -0.690     A    3.29632525712e-01
>   8.368000e-01
>     OG2D1     8    15.9994     -0.580     A    3.02905564168e-01
>   5.020800e-01 ;   2.49451641079e-01    5.020800e-01
>
> [ bondtypes ]
> ; i j func b0 Kb
>    CG2O6   NG2S2     1  1.360000e-01  3.598240e+05
>    CG2O6   OG2D1     1  1.230000e-01  5.439200e+05
>    NG2S2    HGP1     1  1.000000e-01  4.016640e+05
>
> [ pairtypes ]
> ; i j func sigma1-4 epsilon1-4
>    CG2O6   OG2D1     1  3.02905564168e-01  3.83469934154e-01
>     HGP1   OG2D1     1  1.44726496762e-01  3.10857403193e-01
>    NG2S2   OG2D1     1  2.89542083396e-01  6.48182492821e-01
>    OG2D1   OG2D1     1  2.49451641079e-01  5.02080000000e-01
>
> [ angletypes ]
> ; i j k func th0 cth S0 Kub
>    CG2O6   NG2S2    HGP1     5  1.2000000e+02  4.1840000e+02  0.0000000e+00
>   0.0000000e+00
>     HGP1   NG2S2    HGP1     5  1.2000000e+02  1.9246400e+02  0.0000000e+00
>   0.0000000e+00
>    NG2S2   CG2O6   NG2S2     5  1.1500000e+02  5.8576000e+02  0.0000000e+00
>   0.0000000e+00
>    NG2S2   CG2O6   OG2D1     5  1.2250000e+02  6.2760000e+02  2.3700000e-01
>   4.1840000e+04
>
> [ dihedraltypes ]
> ; i j k l func phi0 cp mult
>    NG2S2   CG2O6   NG2S2    HGP1     9  1.800000e+02  6.276000e+00      2
>    OG2D1   CG2O6   NG2S2    HGP1     9  1.800000e+02  5.857600e+00      2
>
> [ dihedraltypes ]
> ; i j k l func q0 cq
>    CG2O6   NG2S2   NG2S2   OG2D1     2  0.000000e+00  6.694400e+02
> ............................................................................................................................
> [ atomtypes ]
> ; name at.num mass charge ptype sigma epsilon ; sigma_14 epsilon_14
>      HGP1     1     1.0080      0.369     A    4.00013524445e-02
>   1.924640e-01
>     NG2D1     7    14.0070     -0.370     A    3.29632525712e-01
>   8.368000e-01
>     OG2D1     8    15.9994      0.001     A    3.02905564168e-01
>   5.020800e-01 ;   2.49451641079e-01    5.020800e-01
>
> [ bondtypes ]
> ; i j func b0 Kb
>    NG2D1    HGP1     1  1.000000e-01  3.807440e+05
>    NG2D1   OG2D1     1  1.225000e-01  4.853440e+05
>
> [ pairtypes ]
> ; i j func sigma1-4 epsilon1-4
>     HGP1   OG2D1     1  1.44726496762e-01  3.10857403193e-01
>    NG2D1   OG2D1     1  2.89542083396e-01  6.48182492821e-01
>    OG2D1   OG2D1     1  2.49451641079e-01  5.02080000000e-01
>
> [ angletypes ]
> ; i j k func th0 cth S0 Kub
>    OG2D1   NG2D1    HGP1     5  1.1300000e+02  4.1003200e+02  0.0000000e+00
>   0.0000000e+00
> ....................................................................................................................................
> [ defaults ]
> ; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ
> 1 2 yes 1.0 1.0
>
> [ atomtypes ]
> ; name at.num mass charge ptype sigma epsilon ; sigma_14 epsilon_14
>      HGP1     1     1.0080      0.500     A    4.00013524445e-02
>   1.924640e-01
>     OG311     8    15.9994     -0.500     A    3.14487247504e-01
>   8.037464e-01
>
> [ bondtypes ]
> ; i j func b0 Kb
>    OG311    HGP1     1  9.600000e-02  4.560560e+05
>    OG311   OG311     1  1.420000e-01  3.581504e+05
>
> [ angletypes ]
> ; i j k func th0 cth S0 Kub
>    OG311   OG311    HGP1     5  1.0150000e+02  5.0208000e+02  0.0000000e+00
>   0.0000000e+00
>
> [ dihedraltypes ]
> ; i j k l func phi0 cp mult
>     HGP1   OG311   OG311    HGP1     9  0.000000e+00  7.531200e-01      3
> ..................................................................................................................................
> I just combined files into my system itp file (solvated membrane protein)
> Can i simulate these three molecules together?

-- 
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Justin A. Lemkul, Ph.D.
Assistant Professor
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