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

[Peter C. Lai]

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?
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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Peter C. Lai                 | University of Alabama-Birmingham
Programmer/Analyst           | BEC 257
Genetics, Div. of Research   | 1150 10th Avenue South
pcl at uab.edu                  | Birmingham AL 35294-4461
(205) 690-0808               |
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