# Residue Name for C-terminated Amide in CHARMM Force Fields

**URL:** <https://gromacs.bioexcel.eu/t/residue-name-for-c-terminated-amide-in-charmm-force-fields/3406>\
**Category:** User discussions\
**Tags:** forcefield\
**Created:** [January 5, 2022, 6:03pm UTC](https://gromacs.bioexcel.eu/t/residue-name-for-c-terminated-amide-in-charmm-force-fields/3406 "2022-01-05T18:03:59Z")\
**Posts on this page:** 3\
**Page:** 1

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**Author:** ![tim0marshall](https://avatars.discourse-cdn.com/v4/letter/t/5f9b8f/32.png) [@tim0marshall](https://gromacs.bioexcel.eu/u/tim0marshall)\
**Post date:** [January 5, 2022, 6:04pm UTC](https://gromacs.bioexcel.eu/t/residue-name-for-c-terminated-amide-in-charmm-force-fields/3406/1 "2022-01-05T18:04:00Z")

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GROMACS version: 2021.4  
GROMACS modification: No

I am trying to perform MD simulations using CHARMM27 force field via GROMACS 2021.4.  
The input structure file is a .pdb built from sequence using AmberTools20+tleap. The structure is c-terminated with NH2 and, by default, the “amino acid” is named as NHE (see last 5 lines of .pdb below).  
When I attempt to generate GROMACS-required files for simulation, “NHE” residue is not found in the CHARM22 force field residue database. This issue isn’t seen in AMBER force fileds not OPLS as the topology file is buil

I tried changing residue name to “NH2”, the obvious answer, and got no results. I checked the force field rtp, itp and tdb files, and found no solution.  
There might be a simple answer I am missing or not understanding. Perhaps it is the difference in CHARMM’s termini definition and patching, but it seems that amide termination is not there for CHARMM force fields.  
Please let me know if there is a solution.

“”""  
ATOM 138 N NHE 11 24.340 34.120 25.340 1.00 0.00  
ATOM 139 H1 NHE 11 24.450 34.930 25.930 1.00 0.00  
ATOM 140 H2 NHE 11 23.460 33.920 24.870 1.00 0.00  
TER  
ENDMDL  
“”""

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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:** [January 5, 2022, 6:36pm UTC](https://gromacs.bioexcel.eu/t/residue-name-for-c-terminated-amide-in-charmm-force-fields/3406/2 "2022-01-05T18:36:06Z")

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You do not need a special terminal residue for the case of an amidated C-terminus, you simply need to choose CT2 as the terminal patch when prompted by `pdb2gmx`. I will recommend that you upgrade to CHARMM36, unless you have some specific reason for using the old CHARMM22/CMAP parameters. The C36 port is available at [MacKerell Lab](http://mackerell.umaryland.edu/charmm_ff.shtml#gromacs)

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**Author:** ![tim0marshall](https://avatars.discourse-cdn.com/v4/letter/t/5f9b8f/32.png) [@tim0marshall](https://gromacs.bioexcel.eu/u/tim0marshall)\
**Post date:** [January 5, 2022, 6:44pm UTC](https://gromacs.bioexcel.eu/t/residue-name-for-c-terminated-amide-in-charmm-force-fields/3406/3 "2022-01-05T18:44:15Z")

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Thank you so much Dr. Lemkul.  
This isn’t the first time your forum replies have saved me from a headache and it is highly appreciated.