Rtp database - residue mismatch

User discussions
1

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 Errors - Gromacs

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

2

Please provide the full screen output from pdb2gmx.

3

$ gmx pdb2gmx -f dmso.pdb -ignh
:-) GROMACS - gmx pdb2gmx, 2021.4 (-:

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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 Errors - Gromacs

4

Here is the full output: error - c6e77ce0