GROMACS version: 2022.5
GROMACS modification: No
I’ve been trying to run pdb2gmx on DM2 using CHARMM27, but it keep giving me this error:
Fatal error:
Residue 'UNL' not found in residue topology database
This is the whole output for reference, if anyone can help me I would really appreciate it.
debian@DESKTOP-0ESKP0K:~/trial2$ gmx pdb2gmx -f DM2_clean.pdb -o DM2_processed.gro
:-) GROMACS - gmx pdb2gmx, 2022.5-Debian_2022.5_2 (-:
Executable: /usr/bin/gmx
Data prefix: /usr
Working dir: /home/debian/trial2
Command line:
gmx pdb2gmx -f DM2_clean.pdb -o DM2_processed.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: CHARMM27 all-atom force field (CHARM22 plus CMAP for proteins)
9: GROMOS96 43a1 force field
10: GROMOS96 43a2 force field (improved alkane dihedrals)
11: GROMOS96 45a3 force field (Schuler JCC 2001 22 1205)
12: GROMOS96 53a5 force field (JCC 2004 vol 25 pag 1656)
13: GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656)
14: GROMOS96 54a7 force field (Eur. Biophys. J. (2011), 40,, 843-856, DOI: 10.1007/s00249-011-0700-9)
15: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)
8
Using the Charmm27 force field in directory charmm27.ff
Opening force field file /usr/share/gromacs/top/charmm27.ff/watermodels.dat
Select the Water Model:
1: TIP3P TIP 3-point, recommended
2: TIP4P TIP 4-point
3: TIPS3P CHARMM TIP 3-point with LJ on H's
4: TIP5P TIP 5-point (see https://gitlab.com/gromacs/gromacs/-/issues/1348 for issues)
5: SPC simple point charge
6: SPC/E extended simple point charge
7: None
1
going to rename charmm27.ff/aminoacids.r2b
Opening force field file /usr/share/gromacs/top/charmm27.ff/aminoacids.r2b
going to rename charmm27.ff/rna.r2b
Opening force field file /usr/share/gromacs/top/charmm27.ff/rna.r2b
Reading DM2_clean.pdb...
WARNING: all CONECT records are ignored
Read 'DM2 ', 68 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 68 atoms
chain #res #atoms
1 ' ' 1 68
All occupancies are one
All occupancies are one
Opening force field file /usr/share/gromacs/top/charmm27.ff/atomtypes.atp
Reading residue database... (Charmm27)
Opening force field file /usr/share/gromacs/top/charmm27.ff/aminoacids.rtp
Opening force field file /usr/share/gromacs/top/charmm27.ff/dna.rtp
Opening force field file /usr/share/gromacs/top/charmm27.ff/lipids.rtp
Opening force field file /usr/share/gromacs/top/charmm27.ff/rna.rtp
Opening force field file /usr/share/gromacs/top/charmm27.ff/aminoacids.hdb
Opening force field file /usr/share/gromacs/top/charmm27.ff/dna.hdb
Opening force field file /usr/share/gromacs/top/charmm27.ff/lipids.hdb
Opening force field file /usr/share/gromacs/top/charmm27.ff/rna.hdb
Opening force field file /usr/share/gromacs/top/charmm27.ff/aminoacids.n.tdb
Opening force field file /usr/share/gromacs/top/charmm27.ff/dna.n.tdb
Opening force field file /usr/share/gromacs/top/charmm27.ff/rna.n.tdb
Opening force field file /usr/share/gromacs/top/charmm27.ff/aminoacids.c.tdb
Opening force field file /usr/share/gromacs/top/charmm27.ff/dna.c.tdb
Opening force field file /usr/share/gromacs/top/charmm27.ff/rna.c.tdb
Back Off! I just backed up topol.top to ./#topol.top.2#
Processing chain 1 (68 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
-------------------------------------------------------
Program: gmx pdb2gmx, version 2022.5-Debian_2022.5_2
Source file: src/gromacs/gmxpreprocess/resall.cpp (line 617)
Fatal error:
Residue 'UNL' not found in residue topology database
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------
Disclamer: I’m using a windows subsystem for linux.