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GROMACS: gmx pdb2gmx, version 2020.1-Ubuntu-2020.1-1
Executable: /usr/bin/gmx
Data prefix: /usr
Working dir: /mnt/c/users/haten/onedrive/desktop/gromacs_peg
Command line:
gmx pdb2gmx -f Trast_glycan_combo_delH.pdb -o Tglycan.gro
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 force field in directory charmm36.ff
Opening force field file /usr/share/gromacs/top/charmm36.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
3
going to rename charmm36.ff/aminoacids.r2b
Opening force field file /usr/share/gromacs/top/charmm36.ff/aminoacids.r2b
going to rename charmm36.ff/carb.r2b
Opening force field file /usr/share/gromacs/top/charmm36.ff/carb.r2b
going to rename charmm36.ff/cgenff.r2b
Opening force field file /usr/share/gromacs/top/charmm36.ff/cgenff.r2b
going to rename charmm36.ff/ethers.r2b
Opening force field file /usr/share/gromacs/top/charmm36.ff/ethers.r2b
going to rename charmm36.ff/lipid.r2b
Opening force field file /usr/share/gromacs/top/charmm36.ff/lipid.r2b
going to rename charmm36.ff/metals.r2b
Opening force field file /usr/share/gromacs/top/charmm36.ff/metals.r2b
going to rename charmm36.ff/na.r2b
Opening force field file /usr/share/gromacs/top/charmm36.ff/na.r2b
going to rename charmm36.ff/silicates.r2b
Opening force field file /usr/share/gromacs/top/charmm36.ff/silicates.r2b
going to rename charmm36.ff/solvent.r2b
Opening force field file /usr/share/gromacs/top/charmm36.ff/solvent.r2b
Reading Trast_glycan_combo_delH.pdb…
WARNING: all CONECT records are ignored
Read ‘IG GAMMA-1 CHAIN C REGION’, 10396 atoms
Analyzing pdb file
Splitting chemical chains based on TER records or chain id changing.
There are 6 chains and 0 blocks of water and 1340 residues with 10396 atoms
chain #res #atoms
1 ‘C’ 8 99
2 ‘D’ 6 75
3 ‘A’ 449 3461
4 ‘B’ 449 3461
5 ‘E’ 214 1650
6 ‘F’ 214 1650
All occupancies are one
Opening force field file /usr/share/gromacs/top/charmm36.ff/atomtypes.atp
Reading residue database… (Charmm36)
Opening force field file /usr/share/gromacs/top/charmm36.ff/aminoacids.rtp
Opening force field file /usr/share/gromacs/top/charmm36.ff/carb.rtp
Opening force field file /usr/share/gromacs/top/charmm36.ff/cgenff.rtp
Opening force field file /usr/share/gromacs/top/charmm36.ff/ethers.rtp
Opening force field file /usr/share/gromacs/top/charmm36.ff/lipid.rtp
Opening force field file /usr/share/gromacs/top/charmm36.ff/metals.rtp
Opening force field file /usr/share/gromacs/top/charmm36.ff/na.rtp
Opening force field file /usr/share/gromacs/top/charmm36.ff/silicates.rtp
Opening force field file /usr/share/gromacs/top/charmm36.ff/solvent.rtp
Opening force field file /usr/share/gromacs/top/charmm36.ff/aminoacids.hdb
Opening force field file /usr/share/gromacs/top/charmm36.ff/carb.hdb
Opening force field file /usr/share/gromacs/top/charmm36.ff/cgenff.hdb
Opening force field file /usr/share/gromacs/top/charmm36.ff/ethers.hdb
Opening force field file /usr/share/gromacs/top/charmm36.ff/lipid.hdb
Opening force field file /usr/share/gromacs/top/charmm36.ff/metals.hdb
Opening force field file /usr/share/gromacs/top/charmm36.ff/na.hdb
Opening force field file /usr/share/gromacs/top/charmm36.ff/silicates.hdb
Opening force field file /usr/share/gromacs/top/charmm36.ff/solvent.hdb
Opening force field file /usr/share/gromacs/top/charmm36.ff/aminoacids.n.tdb
Opening force field file /usr/share/gromacs/top/charmm36.ff/carb.n.tdb
Opening force field file /usr/share/gromacs/top/charmm36.ff/cgenff.n.tdb
Opening force field file /usr/share/gromacs/top/charmm36.ff/ethers.n.tdb
Opening force field file /usr/share/gromacs/top/charmm36.ff/lipid.n.tdb
Opening force field file /usr/share/gromacs/top/charmm36.ff/metals.n.tdb
Opening force field file /usr/share/gromacs/top/charmm36.ff/na.n.tdb
Opening force field file /usr/share/gromacs/top/charmm36.ff/silicates.n.tdb
Opening force field file /usr/share/gromacs/top/charmm36.ff/solvent.n.tdb
Opening force field file /usr/share/gromacs/top/charmm36.ff/aminoacids.c.tdb
Opening force field file /usr/share/gromacs/top/charmm36.ff/carb.c.tdb
Opening force field file /usr/share/gromacs/top/charmm36.ff/cgenff.c.tdb
Opening force field file /usr/share/gromacs/top/charmm36.ff/ethers.c.tdb
Opening force field file /usr/share/gromacs/top/charmm36.ff/lipid.c.tdb
Opening force field file /usr/share/gromacs/top/charmm36.ff/metals.c.tdb
Opening force field file /usr/share/gromacs/top/charmm36.ff/na.c.tdb
Opening force field file /usr/share/gromacs/top/charmm36.ff/silicates.c.tdb
Opening force field file /usr/share/gromacs/top/charmm36.ff/solvent.c.tdb
Back Off! I just backed up topol.top to ./#topol.top.11#
Processing chain 1 ‘C’ (99 atoms, 8 residues)
Identified residue NAG1 as a starting terminus.
Identified residue FUC8 as a ending terminus.
8 out of 8 lines of specbond.dat converted successfully
Start terminus NAG-1: NH3+
End terminus FUC-8: COO-
Program: gmx pdb2gmx, version 2020.1-Ubuntu-2020.1-1
Source file: src/gromacs/gmxpreprocess/pdb2top.cpp (line 1079)
Fatal error:
atom C not found in buiding block 8FUC while combining tdb and rtp
For more information and tips for troubleshooting, please check the GROMACS
website at Common Errors — GROMACS webpage https://www.gromacs.org documentation
Hello, I do not quite understand this error. I have added all the carbs to convert and corrected my NAGS, but when I go to FUC-8. There is no C:
From hdb.:
FUC 10
1 5 H1 C1 C2 O1 O5
1 2 HO1 O1 C1 C2
1 5 H5 C5 C4 C6 O5
1 5 H2 C2 C1 C3 O2
1 2 HO2 O2 C2 C1
1 5 H3 C3 C2 C4 O3
1 2 HO3 O3 C3 C2
1 5 H4 C4 C3 C5 O4
1 2 HO4 O4 C4 C3
3 4 H6 C6 C5 C4
From rtp:
[ FUC ]
; alpha-L-fucose
[ atoms ]
C1 CC3162 0.3400 1
H1 HCA1 0.0900 1
O1 OC311 -0.6500 1
HO1 HCP1 0.4200 1
C5 CC3163 0.1100 1
H5 HCA1 0.0900 1
O5 OC3C61 -0.4000 1
C2 CC3161 0.1400 2
H2 HCA1 0.0900 2
O2 OC311 -0.6500 2
HO2 HCP1 0.4200 2
C3 CC3161 0.1400 3
H3 HCA1 0.0900 3
O3 OC311 -0.6500 3
HO3 HCP1 0.4200 3
C4 CC3161 0.1400 4
H4 HCA1 0.0900 4
O4 OC311 -0.6500 4
HO4 HCP1 0.4200 4
C6 CC331 -0.2700 5
H61 HCA3 0.0900 5
H62 HCA3 0.0900 5
H63 HCA3 0.0900 5
[ bonds ]
C1 O1
C1 H1
O1 HO1
C1 O5
C1 C2
C2 H2
C2 O2
O2 HO2
C2 C3
C3 H3
C3 O3
O3 HO3
C3 C4
C4 H4
C4 O4
O4 HO4
C4 C5
C5 H5
C5 C6
C6 H61
C6 H62
C6 H63
C5 O5
From my PDB:
| 90 | C1 | C | FUC | C | 8 | 74.507 | 96.779 | 7.802 | 102.15 | 1.0 | |||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 91 | C2 | C | FUC | C | 8 | 75.487 | 96.075 | 8.899 | 71.28 | 1.0 | |||
| 92 | C3 | C | FUC | C | 8 | 76.539 | 95.118 | 8.283 | 80.53 | 1.0 | |||
| 93 | C4 | C | FUC | C | 8 | 77.238 | 95.795 | 7.095 | 89.64 | 1.0 | |||
| 94 | C5 | C | FUC | C | 8 | 76.205 | 96.143 | 6.054 | 106.68 | 1.0 | |||
| 95 | C6 | C | FUC | C | 8 | 76.804 | 96.776 | 4.798 | 126.87 | 1.0 | |||
| 96 | O2 | O | FUC | C | 8 | 74.821 | 95.437 | 9.987 | 71.49 | 1.0 | |||
| 97 | O3 | O | FUC | C | 8 | 77.541 | 94.79 | 9.246 | 81.45 | 1.0 | |||
| 98 | O4 | O | FUC | C | 8 | 77.886 | 96.987 | 7.499 | 84.91 | 1.0 | |||
| 99 | O5 | O | FUC | C | 8 | 75.205 | 97.085 | 6.577 | 89.19 | 1.0 |
How do I fix this?
Thank you,
Heather