[gmx-users] Water molecule can not be settled‏

[zeineb SI CHAIB]

Dear Mark, 

Thank you very much for your help. 

I checked the .itp file of my new parametrized molecule (THF) generated by pdb2gmx and it is not completed (only [atoms] entry, there is no [bonds], [angles] or [dihedrals] entries. Effectively, pdb2gmx failed to generate the topology of the THF.

The thing that I can't understand is that in GROMACS manual they say that the entries [bonds],  [angles]...etc are optional when parametrizing a new molecule so I just added the [atoms] entry in the .rtp file and apparently it's not sufficient for GROMACS to generate the topology! Am I missing something? 

Regards. 

Zeineb.