Charmm modified residue parameters can't be recognized by charmm force field?

aliyasamian · January 23, 2024, 9:22pm

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?

jalemkul · January 23, 2024, 10:48pm

Please post the exact error you are receiving. The entire terminal output is often very informative for issues with pdb2gmx.

aliyasamian · January 24, 2024, 6:27pm

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

jalemkul · January 24, 2024, 6:45pm

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.

aliyasamian · January 25, 2024, 3:14pm

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 (-: