[gmx-users] help on converting charmm/cgenff parameters to gromacs

Mark Abraham Mark.Abraham at anu.edu.au
Thu Apr 7 09:01:47 CEST 2011

On 7/04/2011 3:45 PM, Peter C. Lai wrote:
> Ok I'm now getting the dreaded "Unknown bond_atomtype CG2O5"

On what line of what file? Please copy and paste the whole error 
message. Keeping information back only hurts you :-)


> grompp fatal error. I ran pdb2gmx on a pdb of my ligand and it generated
> a gro and a top file:
> http://pastebin.com/HL3k7EPU for the gro
> http://pastebin.com/y6T4ir7y for the top
> I ran "grompp -f em.mdp -c nonanone.gro -p nonanone.top -o em.tpr"
> CG2O5 and all the other new atoms I added are in the appropriate
> atomtypes.atp file. The forcefield.itp file I added my custom #includes
> for the new parameters.
> How do I go about tracing this?
> the rtp is correct since it wouldn't have been able to map NNON to a gro
> and top file otherwise.
> Here is my forcefield.itp:
> http://pastebin.com/6dTKuqnG
> The two files I custom added were ffgenbonded.itp and ffgennonbonded.itp
> http://pastebin.com/xYvXtbzT
> http://pastebin.com/XXAbmvRH
> Any help would be greatly appreciated...

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