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

[Mark Abraham]

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...