[gmx-users] Atomistic Simulation

panzu sergio.panzuela at estudiante.uam.es
Wed Dec 4 12:16:25 CET 2013

Hello users,

After downloading the toluene.pdb file of a toluene molecule and its
forcefield tolu.itp from "Automated Topology Builder"  and saved in the root

I use the next comand i order to convert the pdb format to .gro :

bash >> g_pdb2gmx -f tolu.pdb -o tolu.gro  -i tolu.itp

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,
 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 (with CMAP) - version 2.0
 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: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)
15: [DEPRECATED] Encad all-atom force field, using full solvent charges
16: [DEPRECATED] Encad all-atom force field, using scaled-down vacuum
17: [DEPRECATED] Gromacs force field (see manual)
18: [DEPRECATED] Gromacs force field with hydrogens for NMR


Using the Gromos53a6 force field in directory gromos53a6.ff

Opening force field file

Select the Water Model:
 1: SPC    simple point charge, recommended
 2: SPC/E  extended simple point charge
 3: None


Opening force field file /usr/share/gromacs/top/gromos53a6.ff/aminoacids.r2b
Reading tolu.pdb...
WARNING: all CONECT records are ignored
Analyzing pdb file
Splitting chemical chains based on TER records or chain id changing.
There are 1 chains and 0 blocks of water and 0 residues with 15 atoms

  chain  #res #atoms
  1 ' '     1     15  

All occupancies are one
Opening force field file /usr/share/gromacs/top/gromos53a6.ff/atomtypes.atp
Atomtype 1
Reading residue database... (gromos53a6)
Opening force field file /usr/share/gromacs/top/gromos53a6.ff/aminoacids.rtp
Using default: not generating all possible dihedrals
Using default: excluding 3 bonded neighbors
Using default: generating 1,4 H--H interactions
Using default: removing impropers on same bond as a proper
Residue 108
Sorting it all out...
Opening force field file /usr/share/gromacs/top/gromos53a6.ff/aminoacids.hdb
Opening force field file
Opening force field file

Back Off! I just backed up topol.top to ./#topol.top.7#
Processing chain 1 (15 atoms, 1 residues)
Warning: Starting residue _I0L0 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 g_pdb2gmx, VERSION 4.5.7
Source code file: /builddir/build/BUILD/gromacs-4.5.7/src/kernel/resall.c,
line: 581

Fatal error:
Residue '_I0L' 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

"You Own the Sun" (Throwing Muses)


I checked the residue "_I0L" and is defined in the tolu.itp

Why do I get this error? Am I missing something??

Thanks in advance!!


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