[gmx-users] multiple dihedrals of P-O bonds

[Anton Feenstra]

Benno Portmann wrote:
> 
> Hi,
> 
> when creating a topology for ATP the dihedrals for -P-OM- or -OS-P-
> dihedrals should be made by two cos(..) functions according the
> forcefield definition in Gromos96 forcefield as well as in gromacs
> forcefield. The
> parameters in ffgmxbon.itp are
> 
> ...
>    OS    P    1     0.000       1.046      3
>    OS    P    1     0.000       3.138      2
> ...
> 
> These both entrys should be added for each dihedral in the evaluation.
> 
> When creating a .tpr file using grompp the first of these two dihedrals
> seems to be overwritten, gmxdump only gives the second dihedral. In
> Gromacs Version 3.1.2. grompp overwrites the "multiple"-dihedals
> noiseless, in Version 3.1.4. it gives warnings. The same happens with
> dihedrals containing "CS"-atomtypes.
> 
> Any suggestions what to do?

You could define explicit parameters in the .rtp or .itp topology
entry for the ATP. You might want to do it with a #define like it
is done for the Gromos ff's, where you #define the parameters in the
ff*bon.itp file, and use it in the 'atp.itp', or the ff*.rtp file.


-- 
Groetjes,

Anton
 ________ ___________________________________________________________
|        | Anton Feenstra                                            |
| .      | Dept. of Pharmacochemistry - Vrije Universiteit Amsterdam |
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