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

[Yang Ye]

Lisong Mao wrote:

>Hi, 
>
>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.
>  
>
use grompp -pp to check whether your addition is effective.

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