[gmx-users] Adding ligand structure information obtained from ATB into the pdb2gmx gro file (obtained using GROMACS)

Mark Abraham mark.j.abraham at gmail.com
Tue Sep 10 11:55:25 CEST 2013

You cannot mix the .gro and .pdb formats within the same file. One
approach is to direct the GROMACS tool to write the output in pdb
format simply by naming the output file with a .pdb suffix. Then you
can do such a pasting operation, and if you've preserved the format
correctly, proceed to use the resulting file in future GROMACS stages.


On Tue, Sep 10, 2013 at 11:10 AM, MUSYOKA THOMMAS
<mutemibiochemistry at gmail.com> wrote:
> Dear Users,
> I am using the ATB web server to build topologies of my ligands.
> I have tried to include the ligand UNITED ATOM STRUCTURE (generated by the
> ATB) into my protein gro file generated by GROMACS by copying the
> information in the lines starting with HETAM to the end of my protein gro
> file and updating the number of molecules at the beginning of the file so
> as to reflect the change.
> However, i am getting an error when i run the editconf command = Fatal
> error: Something is wrong in the coordinate formatting of file
> ../2oul_processed.gro. Note that gro is fixed format.
> My ligand link is =
> http://compbio.biosci.uq.edu.au/atb/download.py?session=14360
> Can anyone tell me how to solve this.
> Thank you
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