# Pdb2gmx does not recognize DNA when used with Force Field 'charm36-jul2022'

**URL:** <https://gromacs.bioexcel.eu/t/pdb2gmx-does-not-recognize-dna-when-used-with-force-field-charm36-jul2022/5462>\
**Category:** User discussions\
**Tags:** forcefield\
**Created:** [December 20, 2022, 7:55pm UTC](https://gromacs.bioexcel.eu/t/pdb2gmx-does-not-recognize-dna-when-used-with-force-field-charm36-jul2022/5462 "2022-12-20T19:55:31Z")\
**Posts on this page:** 3\
**Page:** 1

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**Author:** ![cfaerman](https://avatars.discourse-cdn.com/v4/letter/c/5e9695/32.png) [@cfaerman](https://gromacs.bioexcel.eu/u/cfaerman)\
**Post date:** [December 20, 2022, 7:55pm UTC](https://gromacs.bioexcel.eu/t/pdb2gmx-does-not-recognize-dna-when-used-with-force-field-charm36-jul2022/5462/1 "2022-12-20T19:55:31Z")

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GROMACS version: 2022.4  
GROMACS modification: No  
My questions are below. Here is a bit of background:

I have run successfully pdb2gmx with the Force Field ‘amber03’. The pdb entry is 5kkq  
I have downloaded the Force Field ‘charm36-jul2022’ and it throws an error while trying to read the DNA within 5kkq …  
'Fatal error:  
atom N not found in building block 1DT while combining tdb and rtp

1. Has anyone else had problems with ‘charm36’?
2. My friend Vis K. suggested that I add the option -ter to the command containing pdb2gmx but I would like to find an answer that does not involve manual inputs as we are planning to automate this process.  
Does anyone have additional suggestions?
3. Is there a way to add ‘charm36-jul2022’ to the GROMACS installation directory? Would this solve this issue?  
Thank you in advance !  
CHF

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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:** [December 20, 2022, 9:30pm UTC](https://gromacs.bioexcel.eu/t/pdb2gmx-does-not-recognize-dna-when-used-with-force-field-charm36-jul2022/5462/2 "2022-12-20T21:30:02Z")

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You need to manually select termini whenever using the CHARMM36 force field. You can automate this via `echo` like any other non-interactive selection in GROMACS.

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**Author:** ![cfaerman](https://avatars.discourse-cdn.com/v4/letter/c/5e9695/32.png) [@cfaerman](https://gromacs.bioexcel.eu/u/cfaerman)\
**Post date:** [December 21, 2022, 3:40am UTC](https://gromacs.bioexcel.eu/t/pdb2gmx-does-not-recognize-dna-when-used-with-force-field-charm36-jul2022/5462/3 "2022-12-21T03:40:38Z")

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Thank you for your reply: quite helpful