# Running MD for capped protein using Charm36 (charmm36\_ljpme-jul2022.ff)

**URL:** <https://gromacs.bioexcel.eu/t/running-md-for-capped-protein-using-charm36-charmm36-ljpme-jul2022-ff/10387>\
**Category:** User discussions\
**Tags:** mdrun\
**Created:** [October 21, 2024, 7:18am UTC](https://gromacs.bioexcel.eu/t/running-md-for-capped-protein-using-charm36-charmm36-ljpme-jul2022-ff/10387 "2024-10-21T07:18:47Z")\
**Posts on this page:** 3\
**Page:** 1

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**Author:** ![Prakhar](https://avatars.discourse-cdn.com/v4/letter/p/7cd45c/32.png) [@Prakhar](https://gromacs.bioexcel.eu/u/Prakhar)\
**Post date:** [October 21, 2024, 7:18am UTC](https://gromacs.bioexcel.eu/t/running-md-for-capped-protein-using-charm36-charmm36-ljpme-jul2022-ff/10387/1 "2024-10-21T07:18:47Z")

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GROMACS version: 2022.3  
GROMACS modification: Yes/No

Hello,  
I am trying to run MD for capped protein using Chamm36 forcefield (charmm36\_ljpme-jul2022.ff). I need to select terminus residue from the following options:

Select start terminus type for ACE-0  
0: NH3+  
1: NH2  
2: HYD1  
3: MET1  
4: 5TER  
5: 5MET  
6: 5PHO  
7: 5POM  
8: None

Select end terminus type for NME-496  
0: COO-  
1: COOH  
2: CT2  
3: CT1  
4: HYD2  
5: MET2  
6: 3TER  
7: None

Kindly advice which option to choose

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<div class="post-metadata">

**Author:** ![slovas](https://avatars.discourse-cdn.com/v4/letter/s/e274bd/32.png) [@slovas](https://gromacs.bioexcel.eu/u/slovas)\
**Post date:** [October 21, 2024, 2:40pm UTC](https://gromacs.bioexcel.eu/t/running-md-for-capped-protein-using-charm36-charmm36-ljpme-jul2022-ff/10387/2 "2024-10-21T14:40:05Z")

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Add the N-acetyl and N-methylamide protection to the N- and C-terminus, respectively, in a structure editor and select “None” for both

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<div class="post-metadata">

**Author:** ![Prakhar](https://avatars.discourse-cdn.com/v4/letter/p/7cd45c/32.png) [@Prakhar](https://gromacs.bioexcel.eu/u/Prakhar)\
**Post date:** [November 1, 2024, 9:29am UTC](https://gromacs.bioexcel.eu/t/running-md-for-capped-protein-using-charm36-charmm36-ljpme-jul2022-ff/10387/3 "2024-11-01T09:29:38Z")

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Hi slovas,

Thank you for your help. I tried that but following error pops up;

Program: gmx pdb2gmx, version 2022.3  
Source file: src/gromacs/gmxpreprocess/pdb2top.cpp (line 1096)

Fatal error:  
There is a dangling bond at at least one of the terminal ends. Fix your  
coordinate file, add a new terminal database entry (.tdb), or select the  
proper existing terminal entry.

For more information and tips for troubleshooting, please check the GROMACS  
website at [Common Errors — GROMACS webpage https://www.gromacs.org documentation](http://www.gromacs.org/Documentation/Errors)