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

Justin A. Lemkul jalemkul at vt.edu
Sat Jun 9 14:57:05 CEST 2012

On 6/9/12 8:53 AM, ramaraju801 wrote:
> @ Mark,
> i added -ter to pdb2gmx command and produced the topology file but still the
> energy minimization step in vacuum  is producing the same error
> @justin
> am presently running the simulation step i.e energy minimization of
> structure in vacuum.
> when producing the topology file ,it gave errors saying some of the atoms
> are missing in atomtypes which i gave ,
> you said atoms shouldn't be added which were not in the first place then can
> u tell me the alternative.

Not without the exact error, copied and pasted from the terminal.  If you're 
working with a simple protein with canonical amino acids, changing an .rtp file 
(or anything else in the force field) is never required.



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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