[gmx-users] new molecule.itp problem

[Shavkat Mamatkulov]

Dear Gromacs users,

I have create a new molecule something like monoatomic polymer chain
(without pdb2gmx):

  C-C-C-C-....-C

included my molecule.itp into topology file:

; Include forcefield parameters
#include "ffG43a1.itp"
#include "newmolecule.itp"

and runned job: box containing  two molecule .  It seems to be working.
But when i have dissolved this
molecule in water, water doesn't feel this molecule at all and job is
crushed. In other words the molecule doesn't interact with water molecules.

  Does it mean a bug in molecule.itp or i have lost something else?

Can anyone suggest me what i have to do.

Thank you in advance

Dr. Shavkat Mamatkulov
Sektion Physik,
LMU Theresienstr. 37, 80333
Muenchen
Tel: 49-89-2180 4596
Fax: 49-89-2180 4517
shavkat at theorie.physik.uni-muenchen.de