[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
> 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.
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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