[gmx-users] error

Justin Lemkul jalemkul at vt.edu
Tue Jan 29 17:10:09 CET 2013

On 1/29/13 11:01 AM, az kalsom wrote:
> hi,
> i am using the following
> comamnd
>   pdb2gmx -ff amber99sb -f proteinamber.pdb -o  protei2.pdb -p protein.top
> -water spce -ignh
> and gets the error
> Fatal error:
> Residue 2 named GLU of a molecule in the input file was mapped
> to an entry in the topology database, but the atom CG used in
> that entry is not found in the input file. Perhaps your atom
> and/or residue naming needs to be fixed.
> how to rename it ?

You may or may not have a naming issue.  pdb2gmx is telling you that the 
expected atom (CG) is missing from the input file.  If you have incomplete 
residues, you will need to use some external (non-Gromacs) modeling software to 
rebuild the missing elements of the input file.



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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