[gmx-users] missing parameters in auto-generated topology file?

[Yun Shi]

Hi all,

I used pdb2gmx and selected amber99sb for generation of itp files of a
normal peptide within GROMACS 4.5.4.

But I saw that all the bonds, angles, and dihedral parameters (c0, c1, c2
...) were not present in the itp file, while only funct is defined. It seems
the same thing happens with opls ff.

So I wonder if those parameters are automatically generated according to
corresponding atom types when implementing grompp? What would happen if I
have exotic species and some atomic sequences are not defined in the   [
angletypes ] or   [ dihedraltypes ] section of amber99sb.ff/ffboned.itp ?


In the other case, when I used amb2gmx.pl to convert glycam force
field-parametized prmtop file to gromacs top file, I saw something like:

[ dihedrals ]
;i  j   k  l     func   C0  ...  C5
    19   18   20   21     3     0.75312     2.25936     0.00000
-3.01248     0.00000     0.00000     ;
    41   1    18   19     3     0.20920     0.62760     0.00000
-0.83680     0.00000     0.00000     ;



Although I understand '3' in the fifth column indicates a
Ryckaert-Bellemans-potential function, but what parameters are those numbers
followed (0.75312     2.25936     0.00000    -3.01248     0.00000
0.00000) correspond to?

Thanks for any help!

Yun
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