# Charmm36-jul2022.ff

**URL:** <https://gromacs.bioexcel.eu/t/charmm36-jul2022-ff/7806>\
**Category:** User discussions\
**Created:** [December 6, 2023, 5:16pm UTC](https://gromacs.bioexcel.eu/t/charmm36-jul2022-ff/7806 "2023-12-06T17:16:57Z")\
**Posts on this page:** 5\
**Page:** 1

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**Author:** ![Roger](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/roger/32/1992_2.png) [@Roger](https://gromacs.bioexcel.eu/u/Roger)\
**Post date:** [December 6, 2023, 5:16pm UTC](https://gromacs.bioexcel.eu/t/charmm36-jul2022-ff/7806/1 "2023-12-06T17:16:58Z")

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GROMACS version:  
GROMACS modification: Yes/No  
Here post your question I am trying to generate amylin 2L86.top using CHARMM36-jul2022.ff and TIP3P. Amylin has 37 residues but the last NH2 is considered as residue 38. Although AMBERsb-star-ILDN.ff works with 38 resiues", Charmm36-jul2022 does not work (see below):  
Fatal error:  
Residue type ‘NH2’ not found in residue topology database.

How to solve this problem?  
Thanks

MacBook-Pro-de-test:Desktop Roger$ gmx pdb2gmx -f 2L86.pdb -o 2L86\_GMX.pdb -p 2L86.top \< \<(echo “1”; echo “1”;)  
:-) GROMACS - gmx pdb2gmx, 2023.3-Homebrew (-:

Executable: /usr/local/bin/../Cellar/gromacs/2023.3/bin/gmx  
Data prefix: /usr/local/bin/../Cellar/gromacs/2023.3  
Working dir: /Users/Roger/Desktop  
Command line:  
gmx pdb2gmx -f 2L86.pdb -o 2L86\_GMX.pdb -p 2L86.top

Select the Force Field:

From current directory:

1: CHARMM all-atom force field

From ‘/usr/local/bin/../Cellar/gromacs/2023.3/share/gromacs/top’:

2: AMBER03 protein, nucleic AMBER94 (Duan et al., J. Comp. Chem. 24, 1999-2012, 2003)

3: AMBER94 force field (Cornell et al., JACS 117, 5179-5197, 1995)

4: AMBER96 protein, nucleic AMBER94 (Kollman et al., Acc. Chem. Res. 29, 461-469, 1996)

5: AMBER99 protein, nucleic AMBER94 (Wang et al., J. Comp. Chem. 21, 1049-1074, 2000)

6: AMBER99SB protein, nucleic AMBER94 (Hornak et al., Proteins 65, 712-725, 2006)

7: AMBER99SB-ILDN protein, nucleic AMBER94 (Lindorff-Larsen et al., Proteins 78, 1950-58, 2010)

8: AMBERGS force field (Garcia & Sanbonmatsu, PNAS 99, 2782-2787, 2002)

9: CHARMM27 all-atom force field (CHARM22 plus CMAP for proteins)

10: GROMOS96 43a1 force field

11: GROMOS96 43a2 force field (improved alkane dihedrals)

12: GROMOS96 45a3 force field (Schuler JCC 2001 22 1205)

13: GROMOS96 53a5 force field (JCC 2004 vol 25 pag 1656)

14: GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656)

15: GROMOS96 54a7 force field (Eur. Biophys. J. (2011), 40, 843-856, DOI: 10.1007/s00249-011-0700-9)

16: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)

Using the Charmm36-jul2022 force field in directory ./charmm36-jul2022.ff  
Opening force field file ./charmm36-jul2022.ff/watermodels.dat

Select the Water Model:

1: TIP3P CHARMM-modified TIP3P water model (recommended over original TIP3P)

2: TIP3P\_ORIGINAL Original TIP3P water model

3: SPC SPC water model

4: SPCE SPC/E water model

5: TIP5P TIP5P water model

6: TIP4P TIP4P water model

7: TIP4PEW TIP4P/Ew water model

8: None

going to rename ./charmm36-jul2022.ff/aminoacids.r2b  
Opening force field file ./charmm36-jul2022.ff/aminoacids.r2b

going to rename ./charmm36-jul2022.ff/carb.r2b  
Opening force field file ./charmm36-jul2022.ff/carb.r2b

going to rename ./charmm36-jul2022.ff/cgenff.r2b  
Opening force field file ./charmm36-jul2022.ff/cgenff.r2b

going to rename ./charmm36-jul2022.ff/ethers.r2b  
Opening force field file ./charmm36-jul2022.ff/ethers.r2b

going to rename ./charmm36-jul2022.ff/lipid.r2b  
Opening force field file ./charmm36-jul2022.ff/lipid.r2b

going to rename ./charmm36-jul2022.ff/metals.r2b  
Opening force field file ./charmm36-jul2022.ff/metals.r2b

going to rename ./charmm36-jul2022.ff/na.r2b  
Opening force field file ./charmm36-jul2022.ff/na.r2b

going to rename ./charmm36-jul2022.ff/silicates.r2b  
Opening force field file ./charmm36-jul2022.ff/silicates.r2b

going to rename ./charmm36-jul2022.ff/solvent.r2b  
Opening force field file ./charmm36-jul2022.ff/solvent.r2b  
Reading 2L86.pdb…  
Read ‘ISLET AMYLOID POLYPEPTIDE; 5 PEPTIDE’, 537 atoms

Analyzing pdb file  
Splitting chemical chains based on TER records or chain id changing.

There are 1 chains and 0 blocks of water and 38 residues with 537 atoms

chain #res #atoms

1 ‘A’ 38 537

All occupancies are one  
All occupancies are one  
Opening force field file ./charmm36-jul2022.ff/atomtypes.atp

Reading residue database… (Charmm36-jul2022)  
Opening force field file ./charmm36-jul2022.ff/aminoacids.rtp  
Opening force field file ./charmm36-jul2022.ff/carb.rtp  
Opening force field file ./charmm36-jul2022.ff/cgenff.rtp  
Opening force field file ./charmm36-jul2022.ff/ethers.rtp  
Opening force field file ./charmm36-jul2022.ff/lipid.rtp  
Opening force field file ./charmm36-jul2022.ff/metals.rtp  
Opening force field file ./charmm36-jul2022.ff/na.rtp  
Opening force field file ./charmm36-jul2022.ff/silicates.rtp  
Opening force field file ./charmm36-jul2022.ff/solvent.rtp  
Opening force field file ./charmm36-jul2022.ff/aminoacids.hdb  
Opening force field file ./charmm36-jul2022.ff/carb.hdb  
Opening force field file ./charmm36-jul2022.ff/cgenff.hdb  
Opening force field file ./charmm36-jul2022.ff/ethers.hdb  
Opening force field file ./charmm36-jul2022.ff/lipid.hdb  
Opening force field file ./charmm36-jul2022.ff/metals.hdb  
Opening force field file ./charmm36-jul2022.ff/na.hdb  
Opening force field file ./charmm36-jul2022.ff/silicates.hdb  
Opening force field file ./charmm36-jul2022.ff/solvent.hdb  
Opening force field file ./charmm36-jul2022.ff/aminoacids.n.tdb  
Opening force field file ./charmm36-jul2022.ff/carb.n.tdb  
Opening force field file ./charmm36-jul2022.ff/cgenff.n.tdb  
Opening force field file ./charmm36-jul2022.ff/ethers.n.tdb  
Opening force field file ./charmm36-jul2022.ff/lipid.n.tdb  
Opening force field file ./charmm36-jul2022.ff/metals.n.tdb  
Opening force field file ./charmm36-jul2022.ff/na.n.tdb  
Opening force field file ./charmm36-jul2022.ff/silicates.n.tdb  
Opening force field file ./charmm36-jul2022.ff/solvent.n.tdb  
Opening force field file ./charmm36-jul2022.ff/aminoacids.c.tdb  
Opening force field file ./charmm36-jul2022.ff/carb.c.tdb  
Opening force field file ./charmm36-jul2022.ff/cgenff.c.tdb  
Opening force field file ./charmm36-jul2022.ff/ethers.c.tdb  
Opening force field file ./charmm36-jul2022.ff/lipid.c.tdb  
Opening force field file ./charmm36-jul2022.ff/metals.c.tdb  
Opening force field file ./charmm36-jul2022.ff/na.c.tdb  
Opening force field file ./charmm36-jul2022.ff/silicates.c.tdb  
Opening force field file ./charmm36-jul2022.ff/solvent.c.tdb

Back Off! I just backed up 2L86.top to ./#2L86.top.3#

Processing chain 1 ‘A’ (537 atoms, 38 residues)  
Analysing hydrogen-bonding network for automated assignment of histidine  
protonation. 62 donors and 55 acceptors were found.  
There are 86 hydrogen bonds  
Will use HISE for residue 18

Identified residue LYS1 as a starting terminus.

Identified residue NH238 as a ending terminus.

* * *

Program: gmx pdb2gmx, version 2023.3-Homebrew  
Source file: src/gromacs/gmxpreprocess/resall.cpp (line 644)

Fatal error:  
Residue type ‘NH2’ not found in residue topology database

## 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)

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**Author:** ![MagnusL](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/magnusl/32/2380_2.png) [@MagnusL](https://gromacs.bioexcel.eu/u/MagnusL)\
**Post date:** [December 7, 2023, 10:23am UTC](https://gromacs.bioexcel.eu/t/charmm36-jul2022-ff/7806/2 "2023-12-07T10:23:18Z")

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I would suggest checking that your file 2L86.pdb (especially the terminating NH2 atom line) conforms to PDB specifications, especially regarding residue numbers, residue names and atom names.

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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 7, 2023, 2:37pm UTC](https://gromacs.bioexcel.eu/t/charmm36-jul2022-ff/7806/3 "2023-12-07T14:37:12Z")

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NH2 is not a valid residue in the CHARMM force field. If you’re trying to use an amidated C-terminus, choose the CT2 terminus patch when prompted. You will need to delete the NH2 residue from your input coordinate file to avoid the error.

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**Author:** ![Roger](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/roger/32/1992_2.png) [@Roger](https://gromacs.bioexcel.eu/u/Roger)\
**Post date:** [December 7, 2023, 2:59pm UTC](https://gromacs.bioexcel.eu/t/charmm36-jul2022-ff/7806/4 "2023-12-07T14:59:42Z")

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> [@jalemkul](#):
>
> prompted

Dear Prof. Lemkul,  
Indeed, this is what I am trying to do.  
Thanks for the solution!  
Roger

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**Author:** ![Roger](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/roger/32/1992_2.png) [@Roger](https://gromacs.bioexcel.eu/u/Roger)\
**Post date:** [December 7, 2023, 3:08pm UTC](https://gromacs.bioexcel.eu/t/charmm36-jul2022-ff/7806/5 "2023-12-07T15:08:21Z")

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Thanks Dr Lundgorg,  
For the follow up!  
Kindest Regards  
Roger