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

Mark Abraham Mark.Abraham at anu.edu.au
Thu Apr 7 09:44:52 CEST 2011

On 7/04/2011 5:39 PM, Peter C. Lai wrote:
> Actually I figured it out.
> in forcefield.itp,
> the nonbonded.itp file must be included before the bonded.itp file...

Yep, it has the [atomtypes].


> On 2011-04-07 02:22:38AM -0500, Mark Abraham wrote:
>> 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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