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

Gurunath Katagi gurunath.katagi at gmail.com
Sat Jun 9 19:10:14 CEST 2012

why dont u post what u did  along with the part of the structure/file
attached ...
and what is the error  and what u did to rectify...

and as per as i know, if u are working with DNA system along with CHARMM
forcefield, u should be careful with the atom types ...
since u haven't mentioned. i think the O2 part is from DNA and adding that
atom type in aminoacid file (aminoacid.rtp) may not serve ur purpose
please check which part does it belong to ( i think its the temini of DNA)
and provide the proper aliases and use it ..

Thank u

On Sat, Jun 9, 2012 at 6:43 PM, Mark Abraham <Mark.Abraham at anu.edu.au>wrote:

> On 9/06/2012 11:08 PM, ramaraju801 wrote:
>> as i said my system is an protein-DNA complex and the error popped up only
>> for atoms in DNA residues.
> That's about 1% of the detail you'll need to provide in order for it to be
> worth any more of anybody's time helping you :-) See
> http://www.gromacs.org/Support for advice on how to effectively ask for
> help. A complete description of your system contents, and copied and pasted
> input and output is essential. You already know from past threads that your
> termini are an issue, so make sure you focus on those details.
> Mark
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