[gmx-users] help on converting charmm/cgenff parameters to gromacs
Peter C. Lai
pcl at uab.edu
Thu Apr 7 07:45:14 CEST 2011
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:
The two files I custom added were ffgenbonded.itp and ffgennonbonded.itp
Any help would be greatly appreciated...
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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