Hello!
I want to create a box with amino acid and water mixture. I am finding hard time with teh first step to go from .pdb to .gro file. I keep getting errors, how should I proceed to get the proper file? Is there a databank I can rely on?
Thank you!
Please provide the exact error messages, and if they originate from pdb2gmx, please provide the entire terminal output from the program, including the command you issued.
gmx pdb2gmx -f ethanol.pdb -o ethanol.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)
15
Using the Oplsaa force field in directory oplsaa.ff
Opening force field file /usr/share/gromacs/top/oplsaa.ff/watermodels.dat
Select the Water Model:
1: TIP4P TIP 4-point, recommended
2: TIP4PEW TIP 4-point with Ewald
3: TIP3P TIP 3-point
4: TIP5P TIP 5-point (see http://redmine.gromacs.org/issues/1348 for issues)
5: TIP5P TIP 5-point improved for Ewald sums
6: SPC simple point charge
7: SPC/E extended simple point charge
8: None
6
Opening force field file /usr/share/gromacs/top/oplsaa.ff/aminoacids.r2b
Reading ethanol.pdb…
WARNING: all CONECT records are ignored
Read 9 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 9 atoms
chain #res #atoms
1 ’ ’ 1 9
All occupancies are one
Opening force field file /usr/share/gromacs/top/oplsaa.ff/atomtypes.atp
Atomtype 814
Reading residue database… (oplsaa)
Opening force field file /usr/share/gromacs/top/oplsaa.ff/aminoacids.rtp
Residue 52
Sorting it all out…
Opening force field file /usr/share/gromacs/top/oplsaa.ff/aminoacids.hdb
Opening force field file /usr/share/gromacs/top/oplsaa.ff/aminoacids.n.tdb
Opening force field file /usr/share/gromacs/top/oplsaa.ff/aminoacids.c.tdb
Processing chain 1 (9 atoms, 1 residues)
Warning: Starting residue MOL1 in chain not identified as Protein/RNA/DNA.
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 5.1.2
Source code file: /build/gromacs-z6bPBg/gromacs-5.1.2/src/gromacs/gmxpreprocess/resall.c, line: 645
Fatal error:
Residue ‘MOL’ not found in residue topology database
For more information and tips for troubleshooting, please check the GROMACS
website at Common Errors — GROMACS webpage https://www.gromacs.org documentation
This is an extremely common error and you can easily find the solution with a simple Google search. See Common errors when using GROMACS — GROMACS 2022.3 documentation