# Fatal error: atom C1 not found in buiding block 1MET while combining tdb and rtp. error in ignh cmd

**URL:** <https://gromacs.bioexcel.eu/t/fatal-error-atom-c1-not-found-in-buiding-block-1met-while-combining-tdb-and-rtp-error-in-ignh-cmd/5804>\
**Category:** User discussions\
**Created:** [February 15, 2023, 6:12am UTC](https://gromacs.bioexcel.eu/t/fatal-error-atom-c1-not-found-in-buiding-block-1met-while-combining-tdb-and-rtp-error-in-ignh-cmd/5804 "2023-02-15T06:12:51Z")\
**Posts on this page:** 4\
**Page:** 1

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**Author:** ![yukti07](https://avatars.discourse-cdn.com/v4/letter/y/7bcc69/32.png) [@yukti07](https://gromacs.bioexcel.eu/u/yukti07)\
**Post date:** [February 15, 2023, 6:12am UTC](https://gromacs.bioexcel.eu/t/fatal-error-atom-c1-not-found-in-buiding-block-1met-while-combining-tdb-and-rtp-error-in-ignh-cmd/5804/1 "2023-02-15T06:12:51Z")

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GROMACS version: 2018.1  
Here post your question :  
i m trying to run the command: gmx pdb2gmx -f 2n0a.pdb -o 2n0a\_processed.gro -ignh  
i am using the force field: charm 36-july 2022  
water model that is opted is TIP4P.  
whenever i am running this command error shows up:  
Program: gmx pdb2gmx, version 2018.1  
Source file: src/gromacs/gmxpreprocess/pdb2top.cpp (line 1149)

Fatal error:  
atom C1 not found in buiding block 1MET while combining tdb and rtp.

i tried the same command with charm 36-ff feb 2021 and charm-ff 36 july 2021. that does not show any error.  
why is it only showing error in charm 36-ff 2022??

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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:** [February 16, 2023, 2:26pm UTC](https://gromacs.bioexcel.eu/t/fatal-error-atom-c1-not-found-in-buiding-block-1met-while-combining-tdb-and-rtp-error-in-ignh-cmd/5804/2 "2023-02-16T14:26:39Z")

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Choose appropriate termini interactively, as explained here: [Newest CHARMM36 port for GROMACS - #11 by jalemkul](https://gromacs.bioexcel.eu/t/newest-charmm36-port-for-gromacs/868/11)

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**Author:** ![SarthakTrivedi](https://avatars.discourse-cdn.com/v4/letter/s/58956e/32.png) [@SarthakTrivedi](https://gromacs.bioexcel.eu/u/SarthakTrivedi)\
**Post date:** [November 24, 2023, 1:50pm UTC](https://gromacs.bioexcel.eu/t/fatal-error-atom-c1-not-found-in-buiding-block-1met-while-combining-tdb-and-rtp-error-in-ignh-cmd/5804/3 "2023-11-24T13:50:36Z")

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Here, can we assume that the structure of protein isn’t repaired for missing loops properly by chimera web modeller service ?

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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:** [November 24, 2023, 3:05pm UTC](https://gromacs.bioexcel.eu/t/fatal-error-atom-c1-not-found-in-buiding-block-1met-while-combining-tdb-and-rtp-error-in-ignh-cmd/5804/4 "2023-11-24T15:05:14Z")

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The error referred to in this thread has nothing to do with the integrity of a model produced by any software. It’s purely due to a quirk in patch naming in CHARMM that GROMACS doesn’t interpret correctly. If you have an N-terminal MET residue, you MUST interactively select termini to write the topology.