[gmx-users] error in grompp

Justin Lemkul jalemkul at vt.edu
Tue Oct 2 17:32:54 CEST 2012

On 10/2/12 11:26 AM, Shine A wrote:
> Sir,
>      I am studying the dynamics of membrane proteins using KALP-15 in DPPC.
> But grompp (before minimization of system_inflated.gro) giving error like
> this..
> Fatal error:
> Atomtype LC3 not found
> Actually what changes I should do on the system topology, before grompp?
>   I found that atomtype LC3 is found in my dppc.itp file.

If you're following my tutorial, then you have skipped a step or not completed 
the force field modifications.  Go back and ensure that ffnonbonded.itp has been 
modified correctly to include the atom types and parameters from lipid.itp.



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


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