# Problem in file (Broken structure ini.pdb) generated using CGenFF for proceeding in MD Simulation

**URL:** <https://gromacs.bioexcel.eu/t/problem-in-file-broken-structure-ini-pdb-generated-using-cgenff-for-proceeding-in-md-simulation/2926>\
**Category:** User discussions\
**Tags:** mdrun\
**Created:** [October 7, 2021, 8:16am UTC](https://gromacs.bioexcel.eu/t/problem-in-file-broken-structure-ini-pdb-generated-using-cgenff-for-proceeding-in-md-simulation/2926 "2021-10-07T08:16:50Z")\
**Posts on this page:** 1\
**Showing post:** 6

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**Author:** ![deepakshilkar](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/deepakshilkar/32/2612_2.png) [@deepakshilkar](https://gromacs.bioexcel.eu/u/deepakshilkar)\
**Post date:** [November 7, 2023, 10:59am UTC](https://gromacs.bioexcel.eu/t/problem-in-file-broken-structure-ini-pdb-generated-using-cgenff-for-proceeding-in-md-simulation/2926/6 "2023-11-07T10:59:24Z")

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Hi @jalemkul. In my case, the molecule appears fine until the bonds are sorted usi g the perl script. Something goes wrong at when I upload it to CGenFF and the ligand is fragmented. Any clue as to what might be going wrong?

![image](https://europe1.discourse-cdn.com/flex017/uploads/bioexcel1/original/2X/a/aa3bcbe93038fe20e4755f4d22e6870b226d7537.png)

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