[gmx-users] pdb2gmx (ver 5.0.7) - choosing -ter "None" does not work

Peter Stern peter.stern at weizmann.ac.il
Wed Dec 2 21:05:29 CET 2015 

I have had this problem and I suspect that the answer lies in the Fatal error you receive.  Grimace will not allow you to have dangling bonds.  Something has to be attached to the first and last bond, otherwise it is not a viable molecule.

Peter

Sent from my iPad

> On 2 בדצמ׳ 2015, at 18:03, Yoav Atsmon-Raz <yoav.atsmonraz at ucalgary.ca> wrote:
> 
> Hi, I've been trying to make an AAAA peptide with removed amine and Carboxyl terminal groups by applying the -ter "none" option of pdb2gmx.
> However, everytime I apply it, it fails in constructing the gro file. If I don't use the -ter option it suceeds making the gro file but makes those groups itself but I'm looking for a way to avoid that. Thanks in advance for anyone answering this. I'm suspecting that its having problems with applying the "none" option from the .c.tdb and .n.tdb options correctly but i'm not sure how to correct this.
> 
> Following is my output:
> 
> -----------------------------
> GROMACS:      gmx pdb2gmx, VERSION 5.0.7
> Executable:   /usr/local/gromacs/bin/gmx
> Library dir:  /usr/local/gromacs/share/gromacs/top
> Command line:
>  pdb2gmx -f test.pdb -o test -p test.top -ter
> 
> 
> Select the Force Field:
> From '/home/yoav/Programs/Gromacs/gromacs-5.0.7/share/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 /home/yoav/Programs/Gromacs/gromacs-5.0.7/share/top//charmm27.ff
> 
> Opening force field file /home/yoav/Programs/Gromacs/gromacs-5.0.7/share/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 (note: twice as slow in GROMACS)
> 4: TIP5P   TIP 5-point (see http://redmine.gromacs.org/issues/1348 for issues)
> 5: SPC     simple point charge
> 6: SPC/E   extended simple point charge
> 7: None
> 6
> Opening force field file /home/yoav/Programs/Gromacs/gromacs-5.0.7/share/top//charmm27.ff/aminoacids.r2b
> Opening force field file /home/yoav/Programs/Gromacs/gromacs-5.0.7/share/top//charmm27.ff/rna.r2b
> Reading test.pdb...
> Read 40 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 4 residues with 40 atoms
> 
>  chain  #res #atoms
>  1 'A'     4     40
> 
> All occupancies are one
> Opening force field file /home/yoav/Programs/Gromacs/gromacs-5.0.7/share/top//charmm27.ff/atomtypes.atp
> Atomtype 213
> Reading residue database... (charmm27)
> Opening force field file /home/yoav/Programs/Gromacs/gromacs-5.0.7/share/top//charmm27.ff/aminoacids.rtp
> Residue 44
> Sorting it all out...
> Opening force field file /home/yoav/Programs/Gromacs/gromacs-5.0.7/share/top//charmm27.ff/dna.rtp
> Residue 48
> Sorting it all out...
> Opening force field file /home/yoav/Programs/Gromacs/gromacs-5.0.7/share/top//charmm27.ff/lipids.rtp
> Residue 60
> Sorting it all out...
> Opening force field file /home/yoav/Programs/Gromacs/gromacs-5.0.7/share/top//charmm27.ff/rna.rtp
> Residue 64
> Sorting it all out...
> Opening force field file /home/yoav/Programs/Gromacs/gromacs-5.0.7/share/top//charmm27.ff/aminoacids.hdb
> Opening force field file /home/yoav/Programs/Gromacs/gromacs-5.0.7/share/top//charmm27.ff/dna.hdb
> Opening force field file /home/yoav/Programs/Gromacs/gromacs-5.0.7/share/top//charmm27.ff/lipids.hdb
> Opening force field file /home/yoav/Programs/Gromacs/gromacs-5.0.7/share/top//charmm27.ff/rna.hdb
> Opening force field file /home/yoav/Programs/Gromacs/gromacs-5.0.7/share/top//charmm27.ff/aminoacids.n.tdb
> Opening force field file /home/yoav/Programs/Gromacs/gromacs-5.0.7/share/top//charmm27.ff/dna.n.tdb
> Opening force field file /home/yoav/Programs/Gromacs/gromacs-5.0.7/share/top//charmm27.ff/rna.n.tdb
> Opening force field file /home/yoav/Programs/Gromacs/gromacs-5.0.7/share/top//charmm27.ff/aminoacids.c.tdb
> Opening force field file /home/yoav/Programs/Gromacs/gromacs-5.0.7/share/top//charmm27.ff/dna.c.tdb
> Opening force field file /home/yoav/Programs/Gromacs/gromacs-5.0.7/share/top//charmm27.ff/rna.c.tdb
> 
> Back Off! I just backed up test.top to ./#test.top.13#
> Processing chain 1 'A' (40 atoms, 4 residues)
> Identified residue ALA1 as a starting terminus.
> Identified residue ALA4 as a ending terminus.
> 9 out of 9 lines of specbond.dat converted successfully
> Select start terminus type for ALA-1
> 0: NH3+
> 1: NH2
> 2: None
> 2
> Start terminus ALA-1: None
> Select end terminus type for ALA-4
> 0: COO-
> 1: COOH
> 2: CT2
> 3: CT3
> 4: None
> 4
> End terminus ALA-4: None
> 
> -------------------------------------------------------
> Program pdb2gmx, VERSION 5.0.7
> Source code file: /home/yoav/Programs/Gromacs/gromacs-5.0.7/src/gromacs/gmxpreprocess/pdb2top.cpp, line: 1091
> 
> Fatal error:
> There is a dangling bond at at least one of the terminal ends. Fix your coordinate file, add a new terminal database entry (.tdb), or select the proper existing terminal entry.
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> -------------------------------------------------------
> 
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