[gmx-users] Atomistic Simulation

[Justin Lemkul]

On 12/4/13 6:15 AM, panzu wrote:
> 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
> /usr/share/gromacs/top/gromos53a6.ff
>
> 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,
> 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 (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
> charges
> 17: [DEPRECATED] Gromacs force field (see manual)
> 18: [DEPRECATED] Gromacs force field with hydrogens for NMR
>
> 13
>
>
> Using the Gromos53a6 force field in directory gromos53a6.ff
>
> Opening force field file
> /usr/share/gromacs/top/gromos53a6.ff/watermodels.dat
>
> Select the Water Model:
>   1: SPC    simple point charge, recommended
>   2: SPC/E  extended simple point charge
>   3: None
>
> 3
>
> Opening force field file /usr/share/gromacs/top/gromos53a6.ff/aminoacids.r2b
> Reading tolu.pdb...
> WARNING: all CONECT records are ignored
> Read 'ALL ATOM STRUCTURE FOR MOLECULE 0', 15 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 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
> /usr/share/gromacs/top/gromos53a6.ff/aminoacids.n.tdb
> Opening force field file
> /usr/share/gromacs/top/gromos53a6.ff/aminoacids.c.tdb
>
> 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??
>

Why are you running pdb2gmx?  ATB provides you with the topology that you need.

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441

==================================================