# Potential bug in pdb2gmx
**URL:** https://gromacs.bioexcel.eu/t/potential-bug-in-pdb2gmx/12112
**Category:** User discussions
**Tags:** pdb2gmx, forcefield
**Created:** [May 19, 2025, 2:26pm UTC](https://gromacs.bioexcel.eu/t/potential-bug-in-pdb2gmx/12112 "2025-05-19T14:26:56Z")
**Posts on this page:** 2
**Page:** 1
### Author:  [@cheesecake](https://gromacs.bioexcel.eu/u/cheesecake)
#### Post date: [May 19, 2025, 2:26pm UTC](https://gromacs.bioexcel.eu/t/potential-bug-in-pdb2gmx/12112/1 "2025-05-19T14:26:57Z")
GROMACS version: 2023.2 and 2021
GROMACS modification: No
Hello fellow gromacs users, when trying to create a topol.top file using pdb2gmx for a capped, phosphorylated peptide gromacs claims the OT atom of the phosphorylated serine is missing, though only if ACE-LYS-SP0-CT2. ACE-SP0-LYS-CT2 works fine. Yes, I have included SP0 in residuetypes.dat in the working dir and added it to ./charmm36-jul2022.ff/aminoacids.rtp. I mean it works for the 2nd case, so this is weird. I tested both gmx 2023.2 and 2021; same error.
This is the output:
gmx pdb2gmx -f test.pdb -ter -o confout.pdb
:-) GROMACS - gmx pdb2gmx, 2023.2 (-:
Executable: /usr/local/gmx2023/bin/gmx
Data prefix: /usr/local/gmx2023
Command line:
gmx pdb2gmx -f test.pdb -ter -o confout.pdb
Select the Force Field:
From current directory:
1: CHARMM all-atom force field
From ‘/usr/local/gmx2023/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 test.pdb…
Read ‘LYSPSER’, 45 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 3 residues with 45 atoms
chain #res #atoms
1 ‘A’ 3 45
All occupancies are one
All occupancies are one
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
Back Off! I just backed up topol.top to ./#topol.top.3#
Processing chain 1 ‘A’ (45 atoms, 3 residues)
Identified residue ACE1 as a starting terminus.
Identified residue SP03 as a ending terminus.
8 out of 8 lines of specbond.dat converted successfully
Select start terminus type for ACE-1
0: NH3+
1: NH2
2: HYD1
3: MET1
4: 5TER
5: 5MET
6: 5PHO
7: 5POM
8: None
8
Start terminus ACE-1: None
Select end terminus type for SP0-3
0: COO-
1: COOH
2: CT2
3: CT1
4: HYD2
5: MET2
6: 3TER
7: None
2
End terminus SP0-3: CT2
Opening force field file ./charmm36-jul2022.ff/aminoacids.arn
Checking for duplicate atoms…
Generating any missing hydrogen atoms and/or adding termini.
Now there are 3 residues with 46 atoms
Making bonds…
atom OT is missing in residue SP0 3 in the pdb file
atom OT is missing in residue SP0 3 in the pdb file
* * *
Program: gmx pdb2gmx, version 2023.2
Source file: src/gromacs/gmxpreprocess/pdb2top.cpp (line 1567)
Fatal error:
There were 1 missing atoms in molecule Protein\_chain\_A, if you want to use
this incomplete topology anyhow, use the option -missing
## 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)
This is the pdb that doesn’t work but CLEARLY has the OT atom:
COMPND LYSPSER
AUTHOR GENERATED BY OPEN BABEL 2.4.1
ATOM 1 CH3 ACE A 1 -3.348 4.049 2.023 1.00 0.00 C
ATOM 2 HH31 ACE A 1 -3.494 3.498 2.956 1.00 0.00 H
ATOM 3 HH32 ACE A 1 -4.324 4.205 1.555 1.00 0.00 H
ATOM 4 HH33 ACE A 1 -2.889 5.014 2.255 1.00 0.00 H
ATOM 5 C ACE A 1 -2.461 3.300 1.066 1.00 0.00 C
ATOM 6 O ACE A 1 -2.162 3.740 -0.039 1.00 0.00 O
ATOM 7 N LYS A 2 -2.016 2.081 1.528 1.00 0.00 N
ATOM 8 HN LYS A 2 -2.096 1.880 2.519 1.00 0.00 H
ATOM 9 CA LYS A 2 -1.070 1.293 0.734 1.00 0.00 C
ATOM 10 HA LYS A 2 -1.329 1.419 -0.325 1.00 0.00 H
ATOM 11 CB LYS A 2 0.374 1.765 0.975 1.00 0.00 C
ATOM 12 HB1 LYS A 2 0.745 1.350 1.921 1.00 0.00 H
ATOM 13 HB2 LYS A 2 0.401 2.857 1.085 1.00 0.00 H
ATOM 14 CG LYS A 2 1.317 1.379 -0.172 1.00 0.00 C
ATOM 15 HG1 LYS A 2 1.012 1.905 -1.085 1.00 0.00 H
ATOM 16 HG2 LYS A 2 1.246 0.307 -0.385 1.00 0.00 H
ATOM 17 CD LYS A 2 2.770 1.723 0.159 1.00 0.00 C
ATOM 18 HD1 LYS A 2 3.060 1.227 1.094 1.00 0.00 H
ATOM 19 HD2 LYS A 2 2.864 2.803 0.326 1.00 0.00 H
ATOM 20 CE LYS A 2 3.701 1.287 -0.962 1.00 0.00 C
ATOM 21 HE1 LYS A 2 3.498 1.821 -1.895 1.00 0.00 H
ATOM 22 HE2 LYS A 2 3.655 0.208 -1.138 1.00 0.00 H
ATOM 23 NZ LYS A 2 5.100 1.599 -0.582 1.00 0.00 N
ATOM 24 HZ1 LYS A 2 5.755 1.315 -1.323 1.00 0.00 H
ATOM 25 HZ2 LYS A 2 5.378 1.103 0.276 1.00 0.00 H
ATOM 26 HZ3 LYS A 2 5.236 2.605 -0.420 1.00 0.00 H
ATOM 27 C LYS A 2 -1.244 -0.206 1.059 1.00 0.00 C
ATOM 28 O LYS A 2 -0.321 -1.015 1.017 1.00 0.00 O
ATOM 29 N SP0 A 3 -2.552 -0.590 1.258 1.00 0.00 N
ATOM 30 HN SP0 A 3 -3.267 0.131 1.299 1.00 0.00 H
ATOM 31 CA SP0 A 3 -2.918 -1.970 1.588 1.00 0.00 C
ATOM 32 HA SP0 A 3 -2.389 -2.639 0.897 1.00 0.00 H
ATOM 33 CB SP0 A 3 -2.556 -2.337 3.032 1.00 0.00 C
ATOM 34 HB1 SP0 A 3 -1.516 -2.076 3.253 1.00 0.00 H
ATOM 35 HB2 SP0 A 3 -3.185 -1.781 3.738 1.00 0.00 H
ATOM 36 OG SP0 A 3 -2.687 -3.736 3.220 1.00 0.00 O
ATOM 37 P SP0 A 3 -3.405 -4.236 4.561 1.00 0.00 P
ATOM 38 O1P SP0 A 3 -2.692 -3.885 5.820 1.00 0.00 O
ATOM 39 O2P SP0 A 3 -3.624 -5.798 4.342 1.00 0.00 O
ATOM 40 H2T SP0 A 3 -3.817 -6.236 5.191 1.00 0.00 H
ATOM 41 OT SP0 A 3 -4.887 -3.664 4.438 1.00 0.00 O
ATOM 42 HT SP0 A 3 -5.221 -3.718 3.512 1.00 0.00 H
ATOM 43 C SP0 A 3 -4.426 -2.174 1.335 1.00 0.00 C
ATOM 44 O SP0 A 3 -5.142 -2.950 1.965 1.00 0.00 O
ATOM 45 OXT SP0 A 3 -4.929 -1.514 0.244 1.00 0.00 O
END
and this is the .rtp entry:
[SP0]
;
[atoms]
N NH1 -0.4700 1
HN H 0.3100 1
CA CT1 0.0700 1
HA HB1 0.0900 1
CB CT2 -0.0800 2
HB1 HA2 0.0900 2
HB2 HA2 0.0900 2
OG ON2 -0.6100 2
P P 1.5100 2
O1P ON3 -0.6000 2
O2P ON4 -0.6000 2
H2T HN4 0.4000 2
OT ON4 -0.6000 2
HT HN4 0.4000 2
C C 0.5100 3
O O -0.5100 3
[bonds]
CB CA
OG CB
N HN
N CA
C CA
C +N
CA HA
CB HB1
CB HB2
O C
OG P
P OT
OT HT
P O1P
P O2P
[impropers]
N -C CA HN
C CA +N O
[cmap]
-C N CA C +N
Any help is appreciated thanks :)
---
### Author:  [@cheesecake](https://gromacs.bioexcel.eu/u/cheesecake)
#### Post date: [May 20, 2025, 9:52am UTC](https://gromacs.bioexcel.eu/t/potential-bug-in-pdb2gmx/12112/2 "2025-05-20T09:52:46Z")
Ok I found a fix: For some reason (I couldn’t find the ff parameter file that causes it) gromacs renames ‘OT’ to ‘OXT’ which later gets deleted:
Renaming atom ‘HN’ in residue 2 LYS to ‘H’
Renaming atom ‘HN’ in residue 3 SP0 to ‘H’
Renaming atom ‘OT’ in residue 3 SP0 to ‘OXT’
The aminoacids.arn file causes the HN rename but not the OT rename.
My solution was to change the atom name in the aminoacids.rtp [SP0] (and SP1, SP2) sections and in the pdb to O3P so it wouldn’t get automatically renamed and deleted. Now it finally works.