[gmx-users] topology file for pyrophosphate group??

[Anton Feenstra]

Shang-Te Danny Hsu wrote:
> 
> Dear listers,
> 
> Has anyone been working with phospholipid or other molecules containing
> pyrophosphate group?
> 
>        O   O
>        |   |
>   -C-O-P-O-P-O-C-
>        "   "
>        O   O
> 
> I submitted the coordinates and the text-format to PRODRG server, and
> the outcomes were the same: only one phosphate group was correctly set
> to a net charge -1, and the other one has no partial charge at all. I've
> been looking around the existing topology files, but no such kind of
> functional groups.....

Check again, there is a triphosphate in ATP. Of course you'll need
to hack some things since you have a diphosphate connected to 
carbons on both ends, but that is trivial (I've done it, it only
involves tuning the charges on the middle oxygen).

It definitely is in the GROMOS force field (ffG43* files), but 
probably also in the (old!) GROMACS ff's (ffgmx*).

-- 
Groetjes,

Anton
 ________ ___________________________________________________________
|        | Anton Feenstra                                            |
| .      | Dept. of Pharmacochemistry - Free University Amsterdam    |
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