[gmx-users] problem with the calculation of a propene molecule

[Mark Abraham]

Saskia Frenzel wrote:
> Dear Ladies and Gentlemen,
> 
> I from the University of Applied Sciences in Mittweida currently
> deals with the calculation of a propene molecule using the program
> Gromacs.
> For testing proposer I tried to generate my own force field.
> However, when creating the top-file with this command "grompp_d -f propene.mdp -c propene_new.gro -p propene.top -o propene.tpr -po propene_new.mdp" the following error messages was generated:
> No default Bond types
> No default Angle types
> 
> The original pdb file before adding the water solvent was:
>  
> COMPND      PROPENE
> ATOM      2  C   CH33     1      3.732   0.250   0.000  1.00  0.00
> ATOM      2  H1  CH33     1      4.042  -0.286   0.000  1.00  0.00
> ATOM      2  H2  CH33     1      4.269   0.560   0.000  1.00  0.00
> ATOM      2  H3  CH33     1      3.422   0.786   0.000  1.00  0.00
> ATOM      2  C1  C2H3     2      2.866  -0.250   0.000  1.00  0.00
> ATOM      2  C2  C2H3     2      2.000   0.250   0.000  1.00  0.00
> ATOM      2  H1  C2H3     2      2.866  -0.870   0.000  1.00  0.00
> ATOM      2  H2  C2H3     2      2.000   0.870   0.000  1.00  0.00
> ATOM      2  H3  C2H3     2      1.463  -0.060   0.000  1.00  0.00
>  
> I derived the own force field from ffamber99.
> In the rtp file I have added:
> [CH33]
>  [Atom]
>  C amber99_2 0.880229 1
>  H1 amber99_17 0.395055 2
>  H2 amber99_17 0.395055 3
>  H3 amber99_17 0.395055 4
>  [bonds]
>  C H1
>  C H2
>  C H3
> 
> [C2H3]
>  [Atom]
>  C1 amber99_70 0.880229 1
>  C2 amber99_71 0.880229 2
>  H1 amber99_17 0.395055 3
>  H2 amber99_17 0.395055 4
>  H3 amber99_17 0.395055 5
>  [bonds]
>  C1 C2
>  C1 H1
>  C2 H2
>  C2 H3
>  
> In the itp file we have added:
> [atom type]
>  amber99_70 -> parameters like amber99_2
>  amber99_71 -> parameters like amber99_2
> [bond type]
>  i  j   func  b0      kb
>  C  C1   1    0.1525  259408.0; new99
>  C1 C2   1    0.1525  259408.0; new99
>  C1 H1   1    0.1525  259408.0; new99
>  C2 H2   1    0.1525  259408.0; new99
>  C2 H3   1    0.1525  259408.0; new99
> 
> I would like to ask whether you could help me to solve the problems.
> Also any other hint on the creation/implementation of my own force field is welcome.

Be exacting. Computers are literal. The text of most of your directives 
are not spelled in the way that GROMACS requires. Compare with the 
examples in Chapter 5 of the manual.

Mark