[gmx-users] Atom Types in ffbonded.itp

Justin A. Lemkul jalemkul at vt.edu
Mon May 14 22:45:33 CEST 2012

On 5/14/12 4:38 PM, Lara Bunte wrote:
> Hello
> I want to write my parameters in the ffbonded.itp file in the CHARMM27 force
> field folder. I wrote my atom types in this file. This atom types are defined
> by me in atomtypes.dat

There is no atomtypes.dat that is read by any Gromacs program, and atomtypes.atp 
is not relevant here.

> grompp gives me an error
> Fatal error: Unknown bond_atomtype
> for all my atom types. Do I have to declare that atom types somewhere else
> than in atomtypes.dat?

All atom types need to be present in ffnonbonded.itp, with their parameters 
defined there.  The atom types present in ffnonbonded.itp can then be used in 
bonded interactions defined in ffbonded.itp.



Justin A. Lemkul, Ph.D.
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


More information about the gromacs.org_gmx-users mailing list