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 :-)
Mark
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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