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

[Andy Somogyi]

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.

If the PDB does have missing atoms, can pdb2gmx guess missing atoms like VMD's psf gen?

Any ideas?

thanks