[gmx-users] fetal erorr while running" pdb2gmx" command

Tsjerk Wassenaar tsjerkw at gmail.com
Mon Apr 18 10:40:33 CEST 2011

Hey Sajad,

That sounds quite serious, having a fetal error

But it seems you just have a missing atom, as is indicated in the
output. Check the structure before trying to convert it. In
particular, read the sections in the PDB file starting with 'REMARK
465' and 'REMARK 470'.

Surely you'd also been able to find this in the FAQ or in the
archives. Please search there before posting.

Hope it helps,


On Mon, Apr 18, 2011 at 10:27 AM, Sajad Ahrari <sajadahrari at yahoo.com> wrote:
> dear users
> after running the command "pdb2gmx -f 1OL5.pdb -o 1OL5.gro -water spc" ,i
> was faced with the erorr: "Fatal error: Atom CG not found in residue seq.nr.
> 251 while adding atom". i used Gromacs 4.5.3
> with AMBER99SB force field. it seems that some atomes are missing.should i
> be modeling the protein to have all it's atoms? is Gromacs have any features
> to correct the missing ones?
> thanks!
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Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands

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