# Error when the Parmed package read the gromacs topology file

**URL:** <https://gromacs.bioexcel.eu/t/error-when-the-parmed-package-read-the-gromacs-topology-file/991>\
**Category:** User discussions\
**Created:** [October 21, 2020, 12:58am UTC](https://gromacs.bioexcel.eu/t/error-when-the-parmed-package-read-the-gromacs-topology-file/991 "2020-10-21T00:58:56Z")\
**Posts on this page:** 3\
**Page:** 1

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**Author:** ![Jinyoung](https://avatars.discourse-cdn.com/v4/letter/j/3be4f8/32.png) [@Jinyoung](https://gromacs.bioexcel.eu/u/Jinyoung)\
**Post date:** [October 21, 2020, 12:58am UTC](https://gromacs.bioexcel.eu/t/error-when-the-parmed-package-read-the-gromacs-topology-file/991/1 "2020-10-21T00:58:56Z")

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GROMACS version: 2019.4  
GROMACS modification: Yes

Dear gromacs users,  
I’ve try to use Parmed to convert gromacs topology file into amber prmtop file format.  
But in the my python script `gro_top = pmd.load_file('topol.top')` line, error occured below:  
**parmed.exceptions.MoleculeError: Cannot bond two virtual sites/extra points together**

Because the topology file didn’t have any problem when I run MD simulation, I don’t know why the topology file raised error.  
I make the topology file that I attached by using pdb2gmx with the GROMOS54a7 force field.  
[topol.top](https://gromacs.bioexcel.eu/uploads/short-url/hnGyQNvlbRLnsR70yBSDUwIvaRQ.top) (674.9 KB)

Could you tell me what I’m missing?  
Thank you

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**Author:** ![jalemkul](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/jalemkul/32/18_2.png) [@jalemkul](https://gromacs.bioexcel.eu/u/jalemkul)\
**Post date:** [October 21, 2020, 1:16pm UTC](https://gromacs.bioexcel.eu/t/error-when-the-parmed-package-read-the-gromacs-topology-file/991/2 "2020-10-21T13:16:29Z")

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This is an issue with ParmEd and you should contact its authors. Your topology apparently has some setup that their conversion scripts can’t handle.

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**Author:** ![Jinyoung](https://avatars.discourse-cdn.com/v4/letter/j/3be4f8/32.png) [@Jinyoung](https://gromacs.bioexcel.eu/u/Jinyoung)\
**Post date:** [October 22, 2020, 1:37am UTC](https://gromacs.bioexcel.eu/t/error-when-the-parmed-package-read-the-gromacs-topology-file/991/3 "2020-10-22T01:37:56Z")

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Thank you :)