# Charmm modified residue parameters can't be recognized by charmm force field? **URL:** \ **Category:** User discussions\ **Tags:** forcefield\ **Created:** [January 23, 2024, 9:22pm UTC](https://gromacs.bioexcel.eu/t/charmm-modified-residue-parameters-cant-be-recognized-by-charmm-force-field/8117 "2024-01-23T21:22:54Z")\ **Posts on this page:** 8\ **Page:** 1
**Author:** ![aliyasamian](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/aliyasamian/32/2842_2.png) [@aliyasamian](https://gromacs.bioexcel.eu/u/aliyasamian)\ **Post date:** [January 23, 2024, 9:22pm UTC](https://gromacs.bioexcel.eu/t/charmm-modified-residue-parameters-cant-be-recognized-by-charmm-force-field/8117/1 "2024-01-23T21:22:54Z")
Hello I have a question. When i use pdb2gmx, i get error that OMT modified residue can’t be recognized by charmm force field.but when i check charmm36 folder, i found the “aminoacid.rtp” file that contains all of modified residue parameters. Anyway how can I solve my problem?? Why can’t charmm recognize modified residue, while it has all of modified residue parameters in aminoacid.rtp file? ---
**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 23, 2024, 10:48pm UTC](https://gromacs.bioexcel.eu/t/charmm-modified-residue-parameters-cant-be-recognized-by-charmm-force-field/8117/2 "2024-01-23T22:48:40Z")
Please post the exact error you are receiving. The entire terminal output is often very informative for issues with `pdb2gmx`. ---
**Author:** ![aliyasamian](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/aliyasamian/32/2842_2.png) [@aliyasamian](https://gromacs.bioexcel.eu/u/aliyasamian)\ **Post date:** [January 24, 2024, 6:27pm UTC](https://gromacs.bioexcel.eu/t/charmm-modified-residue-parameters-cant-be-recognized-by-charmm-force-field/8117/3 "2024-01-24T18:27:38Z")
gmx pdb2gmx -f 2cag\_clean.pdb -o 2cag\_processed.gro -ter :-) GROMACS - gmx pdb2gmx, 2022.5-Ubuntu\_2022.5\_2ubuntu1 (-: Executable: /usr/bin/gmx Data prefix: /usr Working dir: /home/ali/Downloads/CHARMM OMT Command line: gmx pdb2gmx -f 2cag\_clean.pdb -o 2cag\_processed.gro -ter Select the Force Field: From current directory: 1: CHARMM all-atom force field From ‘/usr/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) 1 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 1 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 2cag\_clean.pdb… WARNING: all CONECT records are ignored Read ‘CATALASE COMPOUND II; 6 CONTAINING THE PROTEIN IN THE COMPOUND I STATE WITH DITHIOTHREITOL’, 3904 atoms Analyzing pdb file Splitting chemical chains based on TER records or chain id changing. Chain identifier ‘A’ is used in two non-sequential blocks. They will be treated as separate chains unless you reorder your file. Chain identifier ‘A’ is used in two non-sequential blocks. They will be treated as separate chains unless you reorder your file. There are 2 chains and 0 blocks of water and 476 residues with 3904 atoms chain #res #atoms 1 ‘A’ 475 3861 2 ‘A’ 1 43 there were 20 atoms with zero occupancy and 0 atoms with occupancy unequal to one (out of 3904 atoms). Check your pdb file. there were 20 atoms with zero occupancy and 0 atoms with occupancy unequal to one (out of 3904 atoms). Check your pdb file. 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 Processing chain 1 ‘A’ (3861 atoms, 475 residues) Analysing hydrogen-bonding network for automated assignment of histidine protonation. 746 donors and 715 acceptors were found. There are 1038 hydrogen bonds Will use HISE for residue 42 Will use HISD for residue 54 Will use HISD for residue 68 Will use HISE for residue 145 Will use HISD for residue 167 Will use HISD for residue 173 Will use HISE for residue 192 Will use HISE for residue 197 Will use HISE for residue 214 Will use HISE for residue 284 Will use HISE for residue 341 Will use HISD for residue 349 Will use HISE for residue 350 Will use HISE for residue 362 Will use HISE for residue 365 Will use HISE for residue 409 Will use HISE for residue 412 Will use HISE for residue 434 Will use HISE for residue 464 * * * Program: gmx pdb2gmx, version 2022.5-Ubuntu\_2022.5\_2ubuntu1 Source file: src/gromacs/gmxpreprocess/pdb2gmx.cpp (line 1040) Fatal error: The residues in the chain LYS4–LEU478 do not have a consistent type. The first residue has type ‘Protein’, while residue OMT53 is of type ‘Other’. Either there is a mistake in your chain, or it includes nonstandard residue names that have not yet been added to the residuetypes.dat file in the GROMACS library directory. If there are other molecules such as ligands, they should not have the same chain ID as the adjacent protein chain since it’s a separate molecule. * * * **END of the error.please pay attention to OMT residue in error.** **Now i add OMT parameters that i copied from CHARMM directory,file aminoacid.rtp.but pdb2gmx can’t recognize OMT** [OMT] ; methionine sulfone [atoms] N NH1 -0.4700 1 HN H 0.3100 1 CA CT1 0.0700 1 HA HB1 0.0900 1 CB CG321 -0.1800 2 HB1 HGA2 0.0900 2 HB2 HGA2 0.0900 2 CG CG321 0.1100 3 HG1 HGA2 0.0900 3 HG2 HGA2 0.0900 3 SD SG3O2 0.1400 3 OE1 OG2P1 -0.3600 3 OE2 OG2P1 -0.3600 3 CE CG331 0.0200 3 HE1 HGA3 0.0900 3 HE2 HGA3 0.0900 3 HE3 HGA3 0.0900 3 C C 0.5100 4 O O -0.5100 4 [bonds] N CA C CA C +N CA HA CA CB N HN CB HB1 CB HB2 CB CG CG HG1 CG HG2 CG SD SD CE CE HE1 CE HE2 CE HE3 O C SD OE1 SD OE2 [impropers] N -C CA HN C CA +N O ---
**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 24, 2024, 6:45pm UTC](https://gromacs.bioexcel.eu/t/charmm-modified-residue-parameters-cant-be-recognized-by-charmm-force-field/8117/4 "2024-01-24T18:45:30Z")
The issue has nothing to do with the CHARMM force field files, actually. They’re working as intended. The problem is that GROMACS relies on a top-level file called `residuetypes.dat` in `$GMXLIB` (`share/top` subdirectory) that defines what kind of residue everything is. If you have modified residues, you have to add them there as the correct biopolymer type. So you need a line that says `OMT Protein` Then `pdb2gmx` will work. ---
**Author:** ![aliyasamian](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/aliyasamian/32/2842_2.png) [@aliyasamian](https://gromacs.bioexcel.eu/u/aliyasamian)\ **Post date:** [January 25, 2024, 3:14pm UTC](https://gromacs.bioexcel.eu/t/charmm-modified-residue-parameters-cant-be-recognized-by-charmm-force-field/8117/5 "2024-01-25T15:14:23Z")
Hello I did what you said exactly but i still receive the same error. I send you a screenshot of the _residuetypes.dat_ and also attach the residuetypes.dat. Now i send you the terminal output: gmx pdb2gmx -f 2cag\_clean.pdb -o 2cag\_processed.gro -ter :-) GROMACS - gmx pdb2gmx, 2023.1-Ubuntu\_2023.1\_2ubuntu1 (-: Executable: /usr/bin/gmx Data prefix: /usr Working dir: /home/ali/Downloads/CHARMM OMT Command line: gmx pdb2gmx -f 2cag\_clean.pdb -o 2cag\_processed.gro -ter Select the Force Field: From current directory: 1: CHARMM all-atom force field From ‘/usr/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) 1 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 1 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 2cag\_clean.pdb… WARNING: all CONECT records are ignored Read ‘’, 3904 atoms Analyzing pdb file Splitting chemical chains based on TER records or chain id changing. Chain identifier ‘A’ is used in two non-sequential blocks. They will be treated as separate chains unless you reorder your file. Chain identifier ‘A’ is used in two non-sequential blocks. They will be treated as separate chains unless you reorder your file. There are 2 chains and 0 blocks of water and 476 residues with 3904 atoms chain #res #atoms 1 ‘A’ 475 3861 2 ‘A’ 1 43 there were 20 atoms with zero occupancy and 0 atoms with occupancy unequal to one (out of 3904 atoms). Check your pdb file. there were 20 atoms with zero occupancy and 0 atoms with occupancy unequal to one (out of 3904 atoms). Check your pdb file. 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 Processing chain 1 ‘A’ (3861 atoms, 475 residues) Analysing hydrogen-bonding network for automated assignment of histidine protonation. 746 donors and 715 acceptors were found. There are 1038 hydrogen bonds Will use HISE for residue 42 Will use HISD for residue 54 Will use HISD for residue 68 Will use HISE for residue 145 Will use HISD for residue 167 Will use HISD for residue 173 Will use HISE for residue 192 Will use HISE for residue 197 Will use HISE for residue 214 Will use HISE for residue 284 Will use HISE for residue 341 Will use HISD for residue 349 Will use HISE for residue 350 Will use HISE for residue 362 Will use HISE for residue 365 Will use HISE for residue 409 Will use HISE for residue 412 Will use HISE for residue 434 Will use HISE for residue 464 * * * Program: gmx pdb2gmx, version 2023.1-Ubuntu\_2023.1\_2ubuntu1 Source file: src/gromacs/gmxpreprocess/pdb2gmx.cpp (line 1042) Fatal error: The residues in the chain LYS4–LEU478 do not have a consistent type. The first residue has type ‘Protein’, while residue OMT53 is of type ‘Other’. Either there is a mistake in your chain, or it includes nonstandard residue names that have not yet been added to the residuetypes.dat file in the GROMACS library directory. If there are other molecules such as ligands, they should not have the same chain ID as the adjacent protein chain since it’s a separate molecule. [residuetypes.dat](https://gromacs.bioexcel.eu/uploads/short-url/z1WnoFYxJV2Lx0q8llMmq1LZ6NC.dat) (2.7 KB) ![Screenshot from 2024-01-25 18-19-06](https://europe1.discourse-cdn.com/flex017/uploads/bioexcel1/original/2X/3/3f42f30197716ce9ce8c66c17779a3289280403d.png) ---
**Author:** ![aliyasamian](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/aliyasamian/32/2842_2.png) [@aliyasamian](https://gromacs.bioexcel.eu/u/aliyasamian)\ **Post date:** [January 27, 2024, 1:34pm UTC](https://gromacs.bioexcel.eu/t/charmm-modified-residue-parameters-cant-be-recognized-by-charmm-force-field/8117/6 "2024-01-27T13:34:42Z")
Hello Do you have any other idea about my problem? Thanks ---
**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 27, 2024, 5:14pm UTC](https://gromacs.bioexcel.eu/t/charmm-modified-residue-parameters-cant-be-recognized-by-charmm-force-field/8117/7 "2024-01-27T17:14:58Z")
The solution is what I said before, but it is not clear to me if you have made (and saved) the edit to `residuetypes.dat` - note that the version in `$GMXLIB` is often write-protected and needs to be edited as an administrator. If you make a copy into your working directory, you can freely edit it and this version and it will be read first. Note that the file must be in the working directory (not the force field subdirectory) for it to be found. ---
**Author:** ![aliyasamian](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/aliyasamian/32/2842_2.png) [@aliyasamian](https://gromacs.bioexcel.eu/u/aliyasamian)\ **Post date:** [January 27, 2024, 9:20pm UTC](https://gromacs.bioexcel.eu/t/charmm-modified-residue-parameters-cant-be-recognized-by-charmm-force-field/8117/8 "2024-01-27T21:20:09Z")
I transferred “residuetypes.dat” to my working directory and my problem is solved. Thank you very much Sir🙏