# Rtp database - residue mismatch
**URL:** https://gromacs.bioexcel.eu/t/rtp-database-residue-mismatch/3497
**Category:** User discussions
**Tags:** pdb2gmx
**Created:** [January 18, 2022, 4:44pm UTC](https://gromacs.bioexcel.eu/t/rtp-database-residue-mismatch/3497 "2022-01-18T16:44:22Z")
**Posts on this page:** 4
**Page:** 1
### Author:  [@KennethG](https://gromacs.bioexcel.eu/u/KennethG)
#### Post date: [January 18, 2022, 4:44pm UTC](https://gromacs.bioexcel.eu/t/rtp-database-residue-mismatch/3497/1 "2022-01-18T16:44:22Z")
GROMACS version: 2021.4
GROMACS modification: No
I want to generate a .gro input file for DMSO using the charmm36 parameters (july2021). When I run pdb2gmx command, I get an error:
$ gmx pdb2gmx -f dmso.pdb
…
Program: gmx pdb2gmx, version 2021.4
Source file: src/gromacs/gmxpreprocess/add\_par.cpp (line 167)
Fatal error:
Atom H2 not found in rtp database in residue DMSO, it looks a bit like H4
## 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)
When checking the input pdb, as well as the rtp file, the H2 atom/atom type is nowhere to be found, so I’m having difficulty in seeing what is going wrong here. Below the pdb file content and the entry in cgenff.rtp:
HETATM 1 O1 DMSO A 1 143.533 121.618 140.585 0.00 0.00 A O
HETATM 2 C3 DMSO A 1 145.879 121.302 139.387 0.00 0.00 A C
HETATM 3 C7 DMSO A 1 144.617 123.713 139.420 0.00 0.00 A C
HETATM 4 S2 DMSO A 1 144.836 122.290 140.485 0.00 0.00 A S
HETATM 5 H4 DMSO A 1 146.856 121.775 139.291 0.00 0.00 A H
HETATM 6 H5 DMSO A 1 145.411 121.234 138.405 0.00 0.00 A H
HETATM 7 H6 DMSO A 1 145.999 120.301 139.803 0.00 0.00 A H
HETATM 8 H8 DMSO A 1 145.565 124.241 139.320 0.00 0.00 A H
HETATM 9 H9 DMSO A 1 143.873 124.381 139.855 0.00 0.00 A H
HETATM 10 H10 DMSO A 1 144.279 123.383 138.438 0.00 0.00 A H
[DMSO]
; C2H6OS, dimethylsulfoxide (ML Strader, et al.JPC2002\_A106\_1074), sz
[atoms]
O1 OG2P1 -0.5500 1
S2 SG3O3 0.3100 1
C3 CG331 -0.1500 1
H4 HGA3 0.0900 1
H5 HGA3 0.0900 1
H6 HGA3 0.0900 1
C7 CG331 -0.1500 1
H8 HGA3 0.0900 1
H9 HGA3 0.0900 1
H10 HGA3 0.0900 1
[bonds]
O1 S2
S2 C3
S2 C7
C3 H4
C3 H5
C3 H6
C7 H8
C7 H9
C7 H10
---
### Author:  [@jalemkul](https://gromacs.bioexcel.eu/u/jalemkul)
#### Post date: [January 19, 2022, 1:47am UTC](https://gromacs.bioexcel.eu/t/rtp-database-residue-mismatch/3497/2 "2022-01-19T01:47:01Z")
Please provide the full screen output from `pdb2gmx`.
---
### Author:  [@KennethG](https://gromacs.bioexcel.eu/u/KennethG)
#### Post date: [January 19, 2022, 6:33am UTC](https://gromacs.bioexcel.eu/t/rtp-database-residue-mismatch/3497/3 "2022-01-19T06:33:50Z")
$ gmx pdb2gmx -f dmso.pdb -ignh
:-) GROMACS - gmx pdb2gmx, 2021.4 (-:
```
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```
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check out [http://www.gromacs.org](http://www.gromacs.org) for more information.
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GROMACS: gmx pdb2gmx, version 2021.4
Executable: /usr/local/gromacs-2021-4/bin/gmx
Data prefix: /usr/local/gromacs-2021-4
Working dir: /home/kenneth/Desktop/Working\_directory/Human\_apoferritin
Command line:
gmx pdb2gmx -f dmso.pdb -ignh
Select the Force Field:
From current directory:
1: CHARMM36 all-atom force field
From ‘/usr/local/gromacs-2021-4/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-jul2021 force field in directory ./charmm36-jul2021.ff
Opening force field file ./charmm36-jul2021.ff/watermodels.dat
Select the Water Model:
1: TIP3P\_CHARMM CHARMM-modified TIP3P water model (recommended over original TIP3P)
2: TIP3P 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
8
going to rename ./charmm36-jul2021.ff/aminoacids.r2b
Opening force field file ./charmm36-jul2021.ff/aminoacids.r2b
going to rename ./charmm36-jul2021.ff/carb.r2b
Opening force field file ./charmm36-jul2021.ff/carb.r2b
going to rename ./charmm36-jul2021.ff/cgenff.r2b
Opening force field file ./charmm36-jul2021.ff/cgenff.r2b
going to rename ./charmm36-jul2021.ff/ethers.r2b
Opening force field file ./charmm36-jul2021.ff/ethers.r2b
going to rename ./charmm36-jul2021.ff/lipid.r2b
Opening force field file ./charmm36-jul2021.ff/lipid.r2b
going to rename ./charmm36-jul2021.ff/metals.r2b
Opening force field file ./charmm36-jul2021.ff/metals.r2b
going to rename ./charmm36-jul2021.ff/na.r2b
Opening force field file ./charmm36-jul2021.ff/na.r2b
going to rename ./charmm36-jul2021.ff/silicates.r2b
Opening force field file ./charmm36-jul2021.ff/silicates.r2b
going to rename ./charmm36-jul2021.ff/solvent.r2b
Opening force field file ./charmm36-jul2021.ff/solvent.r2b
Reading dmso.pdb…
WARNING: all CONECT records are ignored
Read ‘’, 4 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 1 residues with 4 atoms
chain #res #atoms
1 ’ ’ 1 4
All occupancy fields zero. This is probably not an X-Ray structure
All occupancy fields zero. This is probably not an X-Ray structure
Opening force field file ./charmm36-jul2021.ff/atomtypes.atp
Reading residue database… (Charmm36-jul2021)
Opening force field file ./charmm36-jul2021.ff/aminoacids.rtp
Opening force field file ./charmm36-jul2021.ff/carb.rtp
Opening force field file ./charmm36-jul2021.ff/cgenff.rtp
Opening force field file ./charmm36-jul2021.ff/ethers.rtp
Opening force field file ./charmm36-jul2021.ff/lipid.rtp
Opening force field file ./charmm36-jul2021.ff/metals.rtp
Opening force field file ./charmm36-jul2021.ff/na.rtp
Opening force field file ./charmm36-jul2021.ff/silicates.rtp
Opening force field file ./charmm36-jul2021.ff/solvent.rtp
Opening force field file ./charmm36-jul2021.ff/aminoacids.hdb
Opening force field file ./charmm36-jul2021.ff/carb.hdb
Opening force field file ./charmm36-jul2021.ff/cgenff.hdb
Opening force field file ./charmm36-jul2021.ff/ethers.hdb
Opening force field file ./charmm36-jul2021.ff/lipid.hdb
Opening force field file ./charmm36-jul2021.ff/metals.hdb
Opening force field file ./charmm36-jul2021.ff/na.hdb
Opening force field file ./charmm36-jul2021.ff/silicates.hdb
Opening force field file ./charmm36-jul2021.ff/solvent.hdb
Opening force field file ./charmm36-jul2021.ff/aminoacids.n.tdb
Opening force field file ./charmm36-jul2021.ff/carb.n.tdb
Opening force field file ./charmm36-jul2021.ff/cgenff.n.tdb
Opening force field file ./charmm36-jul2021.ff/ethers.n.tdb
Opening force field file ./charmm36-jul2021.ff/lipid.n.tdb
Opening force field file ./charmm36-jul2021.ff/metals.n.tdb
Opening force field file ./charmm36-jul2021.ff/na.n.tdb
Opening force field file ./charmm36-jul2021.ff/silicates.n.tdb
Opening force field file ./charmm36-jul2021.ff/solvent.n.tdb
Opening force field file ./charmm36-jul2021.ff/aminoacids.c.tdb
Opening force field file ./charmm36-jul2021.ff/carb.c.tdb
Opening force field file ./charmm36-jul2021.ff/cgenff.c.tdb
Opening force field file ./charmm36-jul2021.ff/ethers.c.tdb
Opening force field file ./charmm36-jul2021.ff/lipid.c.tdb
Opening force field file ./charmm36-jul2021.ff/metals.c.tdb
Opening force field file ./charmm36-jul2021.ff/na.c.tdb
Opening force field file ./charmm36-jul2021.ff/silicates.c.tdb
Opening force field file ./charmm36-jul2021.ff/solvent.c.tdb
Back Off! I just backed up topol.top to ./#topol.top.9#
Processing chain 1 (4 atoms, 1 residues)
Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior.
8 out of 8 lines of specbond.dat converted successfully
Opening force field file ./charmm36-jul2021.ff/aminoacids.arn
Checking for duplicate atoms…
Generating any missing hydrogen atoms and/or adding termini.
Now there are 1 residues with 10 atoms
Making bonds…
* * *
Program: gmx pdb2gmx, version 2021.4
Source file: src/gromacs/gmxpreprocess/add\_par.cpp (line 167)
Fatal error:
Atom H2 not found in rtp database in residue DMSO, it looks a bit like H4
## 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)
---
### Author:  [@KennethG](https://gromacs.bioexcel.eu/u/KennethG)
#### Post date: [January 19, 2022, 8:27am UTC](https://gromacs.bioexcel.eu/t/rtp-database-residue-mismatch/3497/4 "2022-01-19T08:27:29Z")
Here is the full output: [error - c6e77ce0](https://controlc.com/c6e77ce0)