[gmx-users] Error: dangling bond at atleast one of terminals

[Justin Lemkul]

On 5/9/14, 6:25 AM, Balasubramanian Suriyanarayanan wrote:
> Dear users,
>
>   I am running membrane protein simulation in lipid environment. when I
> processed through pdb2gmx
> *pdb2gmx -f 3B5D.pdb -o 3B5D_processed.gro -ignh -ter -water spc*
>
> *I get the following out put and error. *
>
> *please n*
> *help*
>
> Select the Force Field:
>  From '/opt/bio/gromacs/share/gromacs/top':
>   1: AMBER03 force field (Duan et al., J. Comp. Chem. 24, 1999-2012, 2003)
>   2: AMBER94 force field (Cornell et al., JACS 117, 5179-5197, 1995)
>   3: AMBER96 force field (Kollman et al., Acc. Chem. Res. 29, 461-469, 1996)
>   4: AMBER99 force field (Wang et al., J. Comp. Chem. 21, 1049-1074, 2000)
>   5: AMBER99SB force field (Hornak et al., Proteins 65, 712-725, 2006)
>   6: AMBER99SB-ILDN force field (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
> /opt/bio/gromacs/share/gromacs/top/gromos53a6.ff/aminoacids.r2b
> Reading 3B5D.pdb...
> WARNING: all CONECT records are ignored
> Read 'MULTIDRUG TRANSPORTER EMRE; 5 VIOLOGEN RESISTANCE PROTEIN C, ETHIDIUM
> RESISTANCE PROTEIN', 224 atoms
> Analyzing pdb file
> Splitting PDB chains based on TER records or changing chain id.
> WARNING: Chain identifier 'A' is used in two non-sequential blocks.
> They will be treated as separate chains unless you reorder your file.
> There are 3 chains and 0 blocks of water and 350 residues with 224 atoms
>
>    chain  #res #atoms
>    1 'A'   100    100
>    2 'B'    99     99
>    3 'A'     1     25
>
> All occupancies are one
> Opening force field file
> /opt/bio/gromacs/share/gromacs/top/gromos53a6.ff/atomtypes.atp
> Atomtype 1
> Reading residue database... (gromos53a6)
> Opening force field file
> /opt/bio/gromacs/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
> /opt/bio/gromacs/share/gromacs/top/gromos53a6.ff/aminoacids.hdb
> Opening force field file
> /opt/bio/gromacs/share/gromacs/top/gromos53a6.ff/aminoacids.n.tdb
> Opening force field file
> /opt/bio/gromacs/share/gromacs/top/gromos53a6.ff/aminoacids.c.tdb
>
> Back Off! I just backed up topol.top to ./#topol.top.4#
> Processing chain 1 'A' (100 atoms, 100 residues)
> There are 0 donors and 0 acceptors
> There are 0 hydrogen bonds
> Identified residue TYR6 as a starting terminus.
> Identified residue SER105 as a ending terminus.
> 8 out of 8 lines of specbond.dat converted successfully
> Select start terminus type for TYR-6
>   0: NH3+
>   1: NH2
>   2: None
> 2
> Start terminus TYR-6: None
> Select end terminus type for SER-105
>   0: COO-
>   1: COOH
>   2: None
> 2
> End terminus SER-105: None
>
> -------------------------------------------------------
> Program pdb2gmx, VERSION 4.5.4
> Source code file: pdb2top.c, line: 1035
>
> F*atal error:*
> *There is a dangling bond at at least one of the terminal ends. Select a
> proper terminal entry.*
> *For more information and tips for troubleshooting, please check the
> GROMACS*
> *website at http://www.gromacs.org/Documentation/Errors
> <http://www.gromacs.org/Documentation/Errors>*
>

Choosing "None" for your termini doesn't make sense.  You will have incomplete 
amide groups.

-Justin

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

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA 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
http://mackerell.umaryland.edu/~jalemkul

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