[gmx-users] Atom Types in ffbonded.itp

[Justin A. Lemkul]

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

-- 
========================================

Justin A. Lemkul, Ph.D.
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================