I need to parametrize a ligand which contains an -NO2 group for subsequent simulations with GROMACS. We usually use PRODRG, which despite shortcomings is good enough for our purposes. However, PRODRG does not like -NO2 groups: regardless of how you try to stick the molecule in (drawing, text drawing etc.) it will always complain that the N has too many bonds and stop.
Before going on and doing things by hand, does anybody knows of a server which gives Gromos-compatible topologies and parameters for small molecules?
Thanks! That's for usage with the CHARMM force field rather than the Gromos one we need to use; however it could be very useful, perhaps we can fiddle with the partial charges later. Good.
You can try ATB (http://compbio.biosci.uq.edu.au/atb/?tab=existing_tab).
regards,
Nutan
- Badges
- Science topic