[gmx-users] Fatal error: Atomtype 'K' not found!

Lisong Mao lmao at rufus.biomed.brown.edu
Mon Oct 17 23:33:17 CEST 2005


I was using Gromacs-3.2-1 for peptide simulations. I first used "pdb2gmx" to generate .gro file and I chose 5 from the following options to include H
"Select the Force Field:
 0: GROMOS96 43a1 Forcefield (official distribution)
 1: GROMOS96 43b1 Vacuum Forcefield (official distribution)
 2: GROMOS96 43a2 Forcefield (development) (improved alkane dihedrals)
 3: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)
 4: Gromacs Forcefield (see manual)
 5: gmx Forcefield with hydrogens for NMR stuff (Do NOT use for new runs)"

Then I use "editconf" to generate a box. After I used "grompp -v -f em.mdp -c testbox.gro -o em.tpb -p topol.top" to generate executable for visualization, it gave me an error message 

"creating statusfile for 1 node...

Back Off! I just backed up mdout.mdp to ./#mdout.mdp.1#
checking input for internal consistency...
calling /lib/cpp...
processing topology...
Generated 1232 of the 1431 non-bonded parameter combinations
Cleaning up temporary file gromppvQ9sAC
Fatal error: Atomtype 'K' not found!"

But I don't have K atom in my protein. I add K atom at ffgmx2nb.itp, ffgmx2.rtp, ions.itp files and they won't help.  I know I am using ffgmx2 force field. But what could be the problem at this early stage? Could anyone help me on this? Thanks.

Mao, Ph.D. student
Bio-Med Division
Brown Unversity
Email: lmao at rufus.biomed.brown.edu

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