[gmx-users] Fatal error: Atom CG is used in the topology database...

[Peter C. Lai]

On 2012-03-23 05:39:38PM -0400, Justin A. Lemkul wrote:
> 
> 
> Andy Somogyi wrote:
> > Hi All,
> > 
> > I'm trying to generate topology for a PDB from viperdb, PDB ID 1DZL, http://viperdb.scripps.edu/info_page.php?VDB=1dzl
> > 
> > using 
> > 
> > pdb2gmx -f 1dzl_full.pdb -o test.pdb -p test.top
> > 
> > I've tried CHARMM27 and AMBER03 FFs, water none and I get the result:
> > 
> > Fatal error:
> > Atom CG is used in the topology database, but an atom of that
> > name was not found in residue number 1.
> > 
> > I have not have much luck finding this error in any mailing list.
> > 
> 
> I've never seen that error before, but it sounds like there is an atom named 
> 'CG' in the .rtp entry but not in the coordinate file.  Either the atom is named 
> differently or it is missing.
> 
> > If the PDB does have missing atoms, can pdb2gmx guess missing atoms like VMD's psf gen?
> > 
> 
> No.  The contents of the input coordinate file must match what is expected by 
> the .rtp file.  If you have missing atoms, they must be modeled in using 
> external software.

I wonder if there is a way to overload the hydrogen-adding mechanism to 
add heavy atoms too.

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