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

[Justin A. Lemkul]

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

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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