On 7/04/2011 3:45 PM, Peter C. Lai wrote:
Ok I'm now getting the dreaded "Unknown bond_atomtype CG2O5"
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?
You need to be sure your grompp working directory also has the modified
forcefield file. The "include path" for filenames looks first in the
working directory and then in the directory indicated when you sourced
GMXRC. grompp's normal output (or maybe with -debug 1, or something)
probably says what it is doing.
grompp -pp will write a post-processed stand-alone .top that you can use
to verify things got picked up correctly. However if grompp is failing,
that's probably not a help.
Mark
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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