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

[Saskia Frenzel]

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.

Thank you for your efforts.

Yours sincerely,

Saskia Frenzel

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