[gmx-users] ionomer topolgy

[Ehsan Sadeghi]

Hello Gromacs users,

I am the beginner in Gromacs. I want to simulate ionomer in water. I could not find a pdb file for my case, and I tried to draw the ionomer in Avogadro software and generated the pdb file. However, gmx cannot find my residue names. I added my residue name to residuetypes.dat and added the residue in aminoacids.rtp in gromos. I does not work and it cannot find my new residue. What should I do?

I also have some question regarding the .rtp file. Do you I need to include [ bonds] , [angles], [dihedrals] as well? How can I find charge and charge groups in the [ atoms] section.

Thanks you