Pdb2gmx not recognizing water block

krb0073
Wed, 05 Nov 2025 17:10:03 +0000
User discussions

GROMACS version: 2022.5-Debian_2022.5_2
GROMACS modification: No

Hello all,

I have been trying to create a system using pdb2gmx to generate the topology of a membrane system.

pdb2gmx runs to completion, but the water molecules are not recognized as a separate block. I’ve included the full output of the command at the bottom for reference, but the main issue is summarized below.

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

There are 3 chains and 0 blocks of water and 14264 residues with 69664 atoms

  chain  #res #atoms

  1 ' '   200  27600

  2 ' '    64     64

  3 ' ' 14000  42000

In the PDB file, the system is divided into three chains: (1) lipids, (2) ions, and (3) waters. I’ve verified that the water residue naming follows the CHARMM36 TIP3P convention.
When I use the resulting topology files with gmx grompp, I get the following error:

 gmx grompp -f step6.0_minimization.mdp -c conf.gro -r conf.gro -o min.tpr
Setting the LD random seed to 2138945130

Generated 167799 of the 167910 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 1

Generated 117432 of the 167910 1-4 parameter combinations
ERROR 1 [file topol_Other3.itp, line 98033]:
  No default U-B types


ERROR 2 [file topol_Other3.itp, line 98034]:
  No default U-B types


ERROR 3 [file topol_Other3.itp, line 98036]:
  No default U-B types


ERROR 4 [file topol_Other3.itp, line 98037]:
  No default U-B types


ERROR 5 [file topol_Other3.itp, line 98039]:
  No default U-B types


ERROR 6 [file topol_Other3.itp, line 98040]:
  No default U-B types


ERROR 7 [file topol_Other3.itp, line 98042]:
  No default U-B types


ERROR 8 [file topol_Other3.itp, line 98043]:
  No default U-B types


ERROR 9 [file topol_Other3.itp, line 98045]:
  No default U-B types


ERROR 10 [file topol_Other3.itp, line 98046]:
  No default U-B types

................

ERROR 27989 [file topol_Other3.itp, line 140015]:
  No default U-B types


ERROR 27990 [file topol_Other3.itp, line 140016]:
  No default U-B types


ERROR 27991 [file topol_Other3.itp, line 140018]:
  No default U-B types


ERROR 27992 [file topol_Other3.itp, line 140019]:
  No default U-B types


ERROR 27993 [file topol_Other3.itp, line 140021]:
  No default U-B types


ERROR 27994 [file topol_Other3.itp, line 140022]:
  No default U-B types


ERROR 27995 [file topol_Other3.itp, line 140024]:
  No default U-B types


ERROR 27996 [file topol_Other3.itp, line 140025]:
  No default U-B types


ERROR 27997 [file topol_Other3.itp, line 140027]:
  No default U-B types


ERROR 27998 [file topol_Other3.itp, line 140028]:
  No default U-B types


ERROR 27999 [file topol_Other3.itp, line 140030]:
  No default U-B types


ERROR 28000 [file topol_Other3.itp, line 140031]:
  No default U-B types


-------------------------------------------------------
Program:     gmx grompp, version 2022.5-Debian_2022.5_2
Source file: src/gromacs/gmxpreprocess/grompp.cpp (line 2172)

Fatal error:
There were 28000 errors in input file(s)

For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------

This seems to indicate that the bonded parameters for the TIP3P water molecules (which I haven’t modified) are missing. I find it hard to believe that the CHARMM36 parameters for water are absent from the force field files, so I suspect the issue might originate from the pdb2gmx step.
Interestingly, if I remove the water molecules from the system, both pdb2gmx and grompp complete without major errors.

Thanks for your time,
Kyle

Full gmx pdb2gmx output

 gmx pdb2gmx -f ../step5_input.pdb

Select the Force Field:

From '/usr/share/gromacs/top':

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

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

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

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

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

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

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

 8: CHARMM all-atom force field

 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)
8

Using the Charmm36-jul2022 force field in directory charmm36-jul2022.ff
Opening force field file /usr/share/gromacs/top/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 /usr/share/gromacs/top/charmm36-jul2022.ff/aminoacids.r2b

going to rename charmm36-jul2022.ff/carb.r2b
Opening force field file /usr/share/gromacs/top/charmm36-jul2022.ff/carb.r2b

going to rename charmm36-jul2022.ff/cgenff.r2b
Opening force field file /usr/share/gromacs/top/charmm36-jul2022.ff/cgenff.r2b

going to rename charmm36-jul2022.ff/ethers.r2b
Opening force field file /usr/share/gromacs/top/charmm36-jul2022.ff/ethers.r2b

going to rename charmm36-jul2022.ff/lipid.r2b
Opening force field file /usr/share/gromacs/top/charmm36-jul2022.ff/lipid.r2b

going to rename charmm36-jul2022.ff/metals.r2b
Opening force field file /usr/share/gromacs/top/charmm36-jul2022.ff/metals.r2b

going to rename charmm36-jul2022.ff/na.r2b
Opening force field file /usr/share/gromacs/top/charmm36-jul2022.ff/na.r2b

going to rename charmm36-jul2022.ff/silicates.r2b
Opening force field file /usr/share/gromacs/top/charmm36-jul2022.ff/silicates.r2b

going to rename charmm36-jul2022.ff/solvent.r2b
Opening force field file /usr/share/gromacs/top/charmm36-jul2022.ff/solvent.r2b
Reading ../step5_input.pdb...
Read '', 69664 atoms

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

There are 3 chains and 0 blocks of water and 14264 residues with 69664 atoms

  chain  #res #atoms

  1 ' '   200  27600

  2 ' '    64     64

  3 ' ' 14000  42000

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

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

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

Processing chain 1 (27600 atoms, 200 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 /usr/share/gromacs/top/charmm36-jul2022.ff/aminoacids.arn

Checking for duplicate atoms....

Generating any missing hydrogen atoms and/or adding termini.

Now there are 200 residues with 27600 atoms
Chain time...

Back Off! I just backed up topol_Other.itp to ./#topol_Other.itp.3#

Making bonds...

Number of bonds was 27400, now 27400

Generating angles, dihedrals and pairs...
Before cleaning: 72600 pairs
Before cleaning: 72600 dihedrals

Making cmap torsions...

There are 72600 dihedrals,  400 impropers, 52400 angles
          72600 pairs,     27400 bonds and     0 virtual sites

Total mass 157226.438 a.m.u.

Total charge 0.000 e

Writing topology

Back Off! I just backed up posre_Other.itp to ./#posre_Other.itp.3#

Processing chain 2 (64 atoms, 64 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 /usr/share/gromacs/top/charmm36-jul2022.ff/aminoacids.arn

Checking for duplicate atoms....

Generating any missing hydrogen atoms and/or adding termini.

Now there are 64 residues with 64 atoms
Chain time...

Back Off! I just backed up topol_Other2.itp to ./#topol_Other2.itp.3#

Making bonds...

No bonds

Generating angles, dihedrals and pairs...

Making cmap torsions...

There are    0 dihedrals,    0 impropers,    0 angles
             0 pairs,        0 bonds and     0 virtual sites

Total mass 2385.546 a.m.u.

Total charge 0.000 e

Writing topology

Back Off! I just backed up posre_Other2.itp to ./#posre_Other2.itp.3#

Processing chain 3 (42000 atoms, 14000 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 /usr/share/gromacs/top/charmm36-jul2022.ff/aminoacids.arn

Checking for duplicate atoms....

Generating any missing hydrogen atoms and/or adding termini.

Now there are 14000 residues with 42000 atoms
Chain time...

Back Off! I just backed up topol_Other3.itp to ./#topol_Other3.itp.3#

Making bonds...

Number of bonds was 42000, now 42000

Generating angles, dihedrals and pairs...

Making cmap torsions...

There are    0 dihedrals,    0 impropers, 42000 angles
             0 pairs,     42000 bonds and     0 virtual sites

Total mass 252215.602 a.m.u.

Total charge 0.000 e

Writing topology

Back Off! I just backed up posre_Other3.itp to ./#posre_Other3.itp.3#

Including chain 1 in system: 27600 atoms 200 residues

Including chain 2 in system: 64 atoms 64 residues

Including chain 3 in system: 42000 atoms 14000 residues

Now there are 69664 atoms and 14264 residues

Total mass in system 411827.586 a.m.u.

Total charge in system 0.000 e

Writing coordinate file...

Back Off! I just backed up conf.gro to ./#conf.gro.3#

		--------- PLEASE NOTE ------------

You have successfully generated a topology from: ../step5_input.pdb.

The Charmm36-jul2022 force field and the tip3p water model are used.

		--------- ETON ESAELP ------------

GROMACS reminds you: "Heavier-than-air flying machines are impossible." (Lord Kelvin, President of Royal Society, 1895.)

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