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

[Peter C. Lai]

On 2011-04-07 02:01:47AM -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"
> 
> On what line of what file? Please copy and paste the whole error 
> message. Keeping information back only hurts you :-)

Here is the entire message. It doesn't give me a line number in the
mdp file

NOTE 1 [file em.mdp]:
  For energy conservation with switch/shift potentials, rlist should be 0.1
  to 0.3 nm larger than rcoulomb.


-------------------------------------------------------
Program grompp, VERSION 4.5.4
Source code file: toppush.c, line: 631

Fatal error:
Unknown bond_atomtype CG2O5

For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------


> 
> Mark
> 
> > 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...
> 
> -- 
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

-- 
===============================================================
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               |
===============================================================