[gmx-users] Re: Fatal error: Atomtype O2 not found

Justin A. Lemkul jalemkul at vt.edu
Sat Jun 9 14:35:09 CEST 2012

On 6/9/12 8:31 AM, ramaraju801 wrote:
> correction i added O2 atom to atomtypes.atp file

The atomtypes.atp file is only used by pdb2gmx to make sure it can write certain 
atom types.  If you're introducing a new atom type, its parameters need to go in 
ffnonbonded.itp, and if it is involved in bonded interactions, those need to go 
in ffbonded.itp.  Before doing all that, you should determine whether all that 
effort is needed.  Based on the information at hand, I am still not clear on why 
you think the addition is necessary.



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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