[gmx-users] Need to search parameters.

Mark Abraham mark.j.abraham at gmail.com
Fri Dec 30 09:23:29 CET 2016


Hi,

The meaning of the contents of the files is covered on chapter five of the
reference manual. That's good to understand, but it's more work than you
need to do if your real purpose is just to simulate isobutane with a gromos
force field.

Mark

On Fri, 30 Dec 2016 08:14 Sailesh Bataju <thelaven at gmail.com> wrote:

> Hi,
>
> I need to search parameters like bond length, bond angle, atomic charge,
> dihedral angle, improper dihedral angle and Lennard Jones potential
> parameters like C6 and C12 of isobutane molecule. I've searched those
> parameters in ffbonded.itp and ffnonbonded.itp files inside gromos54a7
> forcefield. Also i've downloaded isobutane.itp for opls forcefield file
> from virtualchemistry.org site but I've no idea how do I extract those
> informations from such files.
>
> Thank you for your guidance.
>
> Isobutane.itp contains
> ; This include topology was generated for the paper below:
> ; Carl Caleman, Paul J. van Maaren, Minyan Hong, Jochen S. Hub,
> ; Luciano T. Costa and David van der Spoel
> ; Force Field Benchmark of Organic Liquids: Density,
> ; Enthalpy of Vaporization, Heat Capacities, Surface Tension,
> ; Isothermal Compressibility, Volumetric Expansion Coefficient,
> ; and Dielectric Constant
> ; J. Chem. Theor. Comput. 8 (2012) 61-74
> ; http://dx.doi.org/10.1021/ct200731v
> ; REFERENCE Caleman2012a
> [ moleculetype ]
>  ; Name            nrexcl
>  isobutane  3
>
>  [ atoms ]
>  ;   nr       type  resnr residue  atom   cgnr     charge       mass  typeB
>    chargeB      massB
>           1  opls_135         1       LIG         C         1     -0.18
>  12.011
>           2  opls_140         1       LIG         H         2      0.06
> 1.008
>           3  opls_140         1       LIG         H         3      0.06
> 1.008
>           4  opls_140         1       LIG         H         4      0.06
> 1.008
>           5  opls_137         1       LIG         C         5     -0.06
>  12.011
>           6  opls_140         1       LIG         H         6      0.06
> 1.008
>           7  opls_135         1       LIG         C         7     -0.18
>  12.011
>           8  opls_140         1       LIG         H         8      0.06
> 1.008
>           9  opls_140         1       LIG         H         9      0.06
> 1.008
>          10  opls_140         1       LIG         H        10      0.06
> 1.008
>          11  opls_135         1       LIG         C        11     -0.18
>  12.011
>          12  opls_140         1       LIG         H        12      0.06
> 1.008
>          13  opls_140         1       LIG         H        13      0.06
> 1.008
>          14  opls_140         1       LIG         H        14      0.06
> 1.008
>
>  [ bonds ]
>  ;  ai    aj funct            c0            c1            c2            c3
>      1     2     1
>      1     3     1
>      1     4     1
>      1     5     1
>      5     6     1
>      5     7     1
>      5    11     1
>      7     8     1
>      7     9     1
>      7    10     1
>     11    12     1
>     11    13     1
>     11    14     1
>
>  [ pairs ]
>  ;  ai    aj funct            c0            c1            c2            c3
>      1     8     1
>      1     9     1
>      1    10     1
>      1    12     1
>      1    13     1
>      1    14     1
>      2     6     1
>      2     7     1
>      2    11     1
>      3     6     1
>      3     7     1
>      3    11     1
>      4     6     1
>      4     7     1
>      4    11     1
>      6     8     1
>      6     9     1
>      6    10     1
>      6    12     1
>      6    13     1
>      6    14     1
>      7    12     1
>      7    13     1
>      7    14     1
>      8    11     1
>      9    11     1
>     10    11     1
>
>  [ angles ]
>  ;  ai    aj    ak funct            c0            c1            c2
>    c3
>      2     1     3     1
>      2     1     4     1
>      2     1     5     1
>      3     1     4     1
>      3     1     5     1
>      4     1     5     1
>      1     5     6     1
>      1     5     7     1
>      1     5    11     1
>      6     5     7     1
>      6     5    11     1
>      7     5    11     1
>      5     7     8     1
>      5     7     9     1
>      5     7    10     1
>      8     7     9     1
>      8     7    10     1
>      9     7    10     1
>      5    11    12     1
>      5    11    13     1
>      5    11    14     1
>     12    11    13     1
>     12    11    14     1
>     13    11    14     1
>
>  [ dihedrals ]
>  ;  ai    aj    ak    al funct            c0            c1            c2
>          c3            c4            c5
>      2     1     5     6     3
>      2     1     5     7     3
>      2     1     5    11     3
>      3     1     5     6     3
>      3     1     5     7     3
>      3     1     5    11     3
>      4     1     5     6     3
>      4     1     5     7     3
>      4     1     5    11     3
>      1     5     7     8     3
>      1     5     7     9     3
>      1     5     7    10     3
>      6     5     7     8     3
>      6     5     7     9     3
>      6     5     7    10     3
>     11     5     7     8     3
>     11     5     7     9     3
>     11     5     7    10     3
>      1     5    11    12     3
>      1     5    11    13     3
>      1     5    11    14     3
>      6     5    11    12     3
>      6     5    11    13     3
>      6     5    11    14     3
>      7     5    11    12     3
>      7     5    11    13     3
>      7     5    11    14     3
>
>
>
> --
> Self-reliant is the great potential for success.
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