[gmx-users] help on converting charmm/cgenff parameters to gromacs
Peter C. Lai
pcl at uab.edu
Thu Apr 7 09:39:56 CEST 2011
Actually I figured it out.
the nonbonded.itp file must be included before the bonded.itp file...
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.
> > 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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