$ 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