[gmx-users] dangling bond error no matter what pdb file I use
asasa qsqs
sanaz_dr_m at yahoo.com
Thu Dec 25 21:58:38 CET 2014
Dear Justin A. Lemkul,
> I want to use pulling code for calculate the PMF of a molecule at the across the
> DMPC, but i can't obtained a large pull across the membrane my pulling code was:
>
> ; Pull code
> pull= umbrella
> pull_geometry= position
> pull_dim= N N Y
> pull_start = yes ; define initial COM distance > 0
> pull_ngroups= 1
> pull_group0= DMPC
> pull_group1= QBH
> pull_k1= 1000 ; kJ mol^-1 nm^-2
> pull_vec1= 0 0 0.5
> after "perl distances.pl" step i obtained a summary.dat file. but in this file
> pulling was very low, just about 0.3nm. My molecule name is QBH and is out of
> membrane at bulk of the water and i want to pull it until center of bilayer.
> what must i do?
On Wednesday, November 5, 2014 1:26 AM, Justin Lemkul <jalemkul at vt.edu> wrote:
On 11/4/14 4:38 PM, Thomas Lipscomb wrote:
> Dear Gromacs mailing list,
>
> I am at this step in a protein in membrane tutorial:
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/01_pdb2gmx.html
>
>
> cd /home/tlipscomb/Desktop/Antimicrobial_Peptides/Gromacs/KALP
> /usr/local/gromacs/bin/gmx pdb2gmx -f 1SG0.pdb -o 1SG0_processed.gro -ignh -ter -water spc
> 13
> 2
> 2
>
> 13 is GROMOS96 53A6
> 2 means no terminus type
>
> I get this error, please help:
>
> -------------------------------------------------------
> Program gmx, VERSION 5.0.1
> Source code file: /home/tlipscomb/gromacs-5.0.1/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
> -------------------------------------------------------
>
>
>
> I know that 1SG0.pdb is correct because it worked for me on DOCK6 and it came from the PDB database. Is it the .tdb file messing up Gromacs? I just installed Gromacs and I thought that the .tdb file it came with is fine.
>
> This is what I have done so far with Gromacs:
> Installed Gromacs on linux
> cd /home/tlipscomb/Desktop/Antimicrobial_Peptides/Gromacs/KALP
> /usr/local/gromacs/bin/gmx pdb2gmx -f 1SG0.pdb -o 1SG0_processed.gro -ignh -ter -water spc
> 13
> 2
> 2
>
> That's it.
>
> Once we resolve this bug I will go back to using model1.pdb (Maximin 3 peptide alpha helix) because that is the protein I need to simulate interacting with the membrane.
>
>
>
> This is the full command line stuff that happened:
>
> [tlipscomb at prime-radiant KALP]$ /usr/local/gromacs/bin/gmx pdb2gmx -f 1SG0.pdb -o 1SG0_processed.gro -ignh -ter -water spc
> GROMACS: gmx pdb2gmx, VERSION 5.0.1
>
> GROMACS is written by:
> Emile Apol Rossen Apostolov Herman J.C. Berendsen Par Bjelkmar
> Aldert van Buuren Rudi van Drunen Anton Feenstra Sebastian Fritsch
> Gerrit Groenhof Christoph Junghans Peter Kasson Carsten Kutzner
> Per Larsson Justin A. Lemkul Magnus Lundborg Pieter Meulenhoff
> Erik Marklund Teemu Murtola Szilard Pall Sander Pronk
> Roland Schulz Alexey Shvetsov Michael Shirts Alfons Sijbers
> Peter Tieleman Christian Wennberg Maarten Wolf
> and the project leaders:
> Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel
>
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> check out http://www.gromacs.org for more information.
>
> GROMACS is free software; you can redistribute it and/or modify it
> under the terms of the GNU Lesser General Public License
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>
> GROMACS: gmx pdb2gmx, VERSION 5.0.1
> Executable: /usr/local/gromacs/bin/gmx
> Library dir: /usr/local/gromacs/share/gromacs/top
> Command line:
> gmx pdb2gmx -f 1SG0.pdb -o 1SG0_processed.gro -ignh -ter -water spc
>
>
> Select the Force Field:
> From '/usr/local/gromacs/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)
> 14
>
> Using the Gromos53a6 force field in directory gromos53a6.ff
>
> Opening force field file /usr/local/gromacs/share/gromacs/top/gromos53a6.ff/aminoacids.r2b
> Reading 1SG0.pdb...
> WARNING: all CONECT records are ignored
> Read 'NRH DEHYDROGENASE [QUINONE] 2; 5 OXIDOREDUCTASE 2', 4143 atoms
> Analyzing pdb file
> Splitting chemical chains based on TER records or chain id changing.
> WARNING: Chain identifier 'A' is used in two non-sequential blocks.
> They will be treated as separate chains unless you reorder your file.
> WARNING: Chain identifier 'B' is used in two non-sequential blocks.
> They will be treated as separate chains unless you reorder your file.
> Moved all the water blocks to the end
> There are 4 chains and 2 blocks of water and 819 residues with 4143 atoms
>
> chain #res #atoms
> 1 'A' 230 1824
> 2 'B' 230 1824
> 3 'A' 3 71
> 4 'B' 3 71
> 5 ' ' 163 163 (only water)
> 6 ' ' 190 190 (only water)
>
> All occupancies are one
> Opening force field file /usr/local/gromacs/share/gromacs/top/gromos53a6.ff/atomtypes.atp
> Atomtype 57
> Reading residue database... (gromos53a6)
> Opening force field file /usr/local/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 proper dihedrals found on the same bond as a proper dihedral
> Residue 108
> Sorting it all out...
> Opening force field file /usr/local/gromacs/share/gromacs/top/gromos53a6.ff/aminoacids.hdb
> Opening force field file /usr/local/gromacs/share/gromacs/top/gromos53a6.ff/aminoacids.n.tdb
> Opening force field file /usr/local/gromacs/share/gromacs/top/gromos53a6.ff/aminoacids.c.tdb
> Processing chain 1 'A' (1824 atoms, 230 residues)
> Analysing hydrogen-bonding network for automated assignment of histidine
> protonation. 341 donors and 337 acceptors were found.
> There are 501 hydrogen bonds
> Will use HISE for residue 11
> Will use HISE for residue 72
> Will use HISE for residue 173
> Will use HISE for residue 177
> Will use HISE for residue 225
> Will use HISD for residue 227
> Identified residue ALA1 as a starting terminus.
> Identified residue GLN230 as a ending terminus.
> 8 out of 8 lines of specbond.dat converted successfully
> Special Atom Distance matrix:
> HIS11 CYS34 MET44 HIS72 MET116 CYS121 MET154
> NE284 SG258 SD332 NE2555 SD923 SG964 SD1202
> CYS34 SG258 2.498
> MET44 SD332 1.591 2.048
> HIS72 NE2555 3.570 3.204 2.500
> MET116 SD923 1.685 2.297 1.437 1.990
> CYS121 SG964 2.870 2.709 1.741 0.763 1.418
> MET154 SD1202 1.814 3.506 3.172 4.279 2.374 3.784
> HIS173 NE21365 2.911 2.892 2.826 2.078 1.469 2.023 2.749
> HIS177 NE21394 3.003 2.433 2.736 2.005 1.588 1.954 3.060
> CYS179 SG1411 2.552 2.310 1.895 1.273 0.924 0.956 3.121
> MET203 SD1594 1.374 2.364 2.587 4.111 2.207 3.533 1.368
> CYS222 SG1753 2.564 2.364 2.567 2.311 1.318 2.104 2.499
> HIS225 NE21775 3.457 3.333 3.854 3.483 2.568 3.414 2.628
> HIS227 NE21799 2.352 2.525 2.625 2.635 1.327 2.365 2.069
> HIS173 HIS177 CYS179 MET203 CYS222 HIS225
> NE21365 NE21394 SG1411 SD1594 SG1753 NE21775
> HIS177 NE21394 0.655
> CYS179 SG1411 1.152 1.046
> MET203 SD1594 2.820 2.833 2.874
> CYS222 SG1753 0.608 0.563 1.150 2.330
> HIS225 NE21775 1.451 1.578 2.475 2.755 1.365
> HIS227 NE21799 0.809 1.002 1.444 2.040 0.450 1.252
> Select start terminus type for ALA-1
> 0: NH3+
> 1: NH2
> 2: None
> 2
> Start terminus ALA-1: None
> Select end terminus type for GLN-230
> 0: COO-
> 1: COOH
> 2: None
> 2
> End terminus GLN-230: None
>
> -------------------------------------------------------
> Program gmx, VERSION 5.0.1
> Source code file: /home/tlipscomb/gromacs-5.0.1/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
> -------------------------------------------------------
>
You haven't added caps onto the input protein, you should expect to get this
error. In the tutorial, I build ACE and NH2 groups onto the peptide to
neutralize the termini. Since you haven't done this type of modification,
pdb2gmx will die because you have incomplete amides at the ends of the chain.
The "None" terminus instructs pdb2gmx to not build additional H (in the case of
NH2 or NH3+ termini) or O(H) (for COO- and COOH). It doesn't make any chemical
sense to use "None" for non-capped protein chains.
-Justin
--
==================================================
Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
==================================================
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