Pdb2gmx - "This chain does not appear to contain a recognized chain molecule." but ion is in the FF

GROMACS version: 2020.4
GROMACS modification: No

I’m hoping for some help running pdb2gmx on a protein which is bound to ADP and Mg2+.

I have ADP and MG on different chains, and both are in the charmm36-feb2021 forcefield .rtp, but I keep getting the following error:

Writing topology

Processing chain 3 ‘I’ (1 atoms, 1 residues)

Residue MG1038 has type ‘Ion’, assuming it is not linked into a chain.

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.

I have included the entire output below for reference. If anyone can help I would really appreciate it! Thanks.


Last login: Mon Sep 13 18:39:44 on ttys000
gmx pdb2gmx -f sm1_ADPMg_start.pdb -o sm1_ADPMg_start_processed.gro
:-) GROMACS - gmx pdb2gmx, 2020.4 (-:

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GROMACS: gmx pdb2gmx, version 2020.4
Executable: /usr/local/gromacs/bin/gmx
Data prefix: /usr/local/gromacs
Working dir: …
Command line:
gmx pdb2gmx -f sm1_ADPMg_start.pdb -o sm1_ADPMg_start_processed.gro

Select the Force Field:
From current directory:
1: CHARMM36 all-atom force field (July 2020)
From ‘/usr/local/gromacs/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-feb2021 force field in directory ./charmm36-feb2021.ff

Opening force field file ./charmm36-feb2021.ff/watermodels.dat

Select the Water Model:
1: TIP3P TIP 3-point, recommended, by default uses CHARMM TIP3 with LJ on H
2: TIP4P TIP 4-point
3: TIP5P TIP 5-point
4: SPC simple point charge
5: SPC/E extended simple point charge
6: None
1
going to rename ./charmm36-feb2021.ff/merged.r2b
Opening force field file ./charmm36-feb2021.ff/merged.r2b
Reading sm1_ADPMg_start.pdb…
Read ‘’, 14436 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 904 residues with 14436 atoms

chain #res #atoms
1 ‘P’ 902 14396
2 ‘H’ 1 39
3 ‘I’ 1 1

All occupancies are one
Opening force field file ./charmm36-feb2021.ff/atomtypes.atp
Reading residue database… (Charmm36-feb2021)
Opening force field file ./charmm36-feb2021.ff/merged.rtp
Opening force field file ./charmm36-feb2021.ff/merged.hdb
Opening force field file ./charmm36-feb2021.ff/merged.n.tdb
Opening force field file ./charmm36-feb2021.ff/merged.c.tdb
Processing chain 1 ‘P’ (14396 atoms, 902 residues)
Identified residue ASP135 as a starting terminus.
Identified residue TRP1036 as a ending terminus.
8 out of 8 lines of specbond.dat converted successfully
Special Atom Distance matrix:

(DID NOT INCLUDE TO SAVE SPACE)

Start terminus ASP-135: NH3+
End terminus TRP-1036: COO-
Opening force field file ./charmm36-feb2021.ff/merged.arn
Checking for duplicate atoms…
Generating any missing hydrogen atoms and/or adding termini.
Now there are 902 residues with 14397 atoms
Chain time…
Making bonds…
Number of bonds was 14534, now 14534
Generating angles, dihedrals and pairs…
Before cleaning: 38175 pairs
Before cleaning: 38495 dihedrals
Keeping all generated dihedrals
Making cmap torsions…
There are 900 cmap torsion pairs
There are 38495 dihedrals, 2510 impropers, 26286 angles
37953 pairs, 14534 bonds and 0 virtual sites
Total mass 102555.718 a.m.u.
Total charge -8.000 e
Writing topology
Processing chain 2 ‘H’ (39 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-feb2021.ff/merged.arn
Checking for duplicate atoms…
Generating any missing hydrogen atoms and/or adding termini.
Now there are 1 residues with 39 atoms
Chain time…
Making bonds…
Number of bonds was 41, now 41
Generating angles, dihedrals and pairs…
Before cleaning: 88 pairs
Before cleaning: 98 dihedrals
Keeping all generated dihedrals
Making cmap torsions…
There are 98 dihedrals, 2 impropers, 71 angles
85 pairs, 41 bonds and 0 virtual sites
Total mass 424.183 a.m.u.
Total charge -3.000 e
Writing topology
Processing chain 3 ‘I’ (1 atoms, 1 residues)
Residue MG1038 has type ‘Ion’, assuming it is not linked into a chain.
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-feb2021.ff/merged.arn
Checking for duplicate atoms…
Generating any missing hydrogen atoms and/or adding termini.
Now there are 1 residues with 1 atoms
Chain time…
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 24.305 a.m.u.
Total charge 2.000 e
Writing topology
Including chain 1 in system: 14397 atoms 902 residues
Including chain 2 in system: 39 atoms 1 residues
Including chain 3 in system: 1 atoms 1 residues
Now there are 14437 atoms and 904 residues
Total mass in system 103004.206 a.m.u.
Total charge in system -9.000 e

Writing coordinate file…
--------- PLEASE NOTE ------------
You have successfully generated a topology from: sm1_ADPMg_start.pdb.
The Charmm36-feb2021 force field and the tip3p water model are used.
--------- ETON ESAELP ------------

GROMACS reminds you: “They don’t have any beavers in India, so they have to simulate them” (The Tubes)

There is no problem here. The program completed successfully. It’s just a verbose message that can help in debugging if you had some kind of modified/custom residue that should be part of a chain but isn’t.

Thanks very much!