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
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