[gmx-users] pdb2gmx do not work for unstable conformations
Mark Abraham
mark.j.abraham at gmail.com
Sat May 20 17:26:17 CEST 2017
Hi,
Some of your PDB files are malformed, which you could see with the less
tool, or probably anything else. The first line, containing N, leads with
strange characters, which stops pdb2gmx recognizing that they start with
"ATOM," since they don't. Then N are recognized as missing.
Mark
On Sat, May 20, 2017 at 3:33 PM ZHANG Cheng <272699575 at qq.com> wrote:
> Dear Gromacs,I have a protein PDB structure as well as its mutants PDB,
> predicted by Rosetta with different ddG. After running pdb2gmx, I found
> that the structures with lower ddG (more stable) all perform okay; while
> structures with higher ddG (less stable) got fatal error:
>
>
> Fatal error:
> Residue 1 named ASP of a molecule in the input file was mapped
> to an entry in the topology database, but the atom N used in
> that entry is not found in the input file. Perhaps your atom
> and/or residue naming needs to be fixed.
>
>
> For example, I got fatal error for:
> gmx pdb2gmx -f HC_V215W.pdb -o HC_V215W_processed.gro -water spce -inter
> -ignh -merge interactive
>
> But it works fine for:
> gmx pdb2gmx -f C226S.pdb -o C226S_processed.gro -water spce -inter -ignh
> -merge interactive
> (just change to another stable mutant, but the first residue ASP is the
> same)
>
>
> But I could not figure out the exact reasons for the fatal error.
>
>
> I have attached two stable PDB and two unstable PDB:
> https://1drv.ms/f/s!AjIs-W_id1LzobIlN0o5fxW49-Fmmg
>
> Could you please help me to find out the reasons?
>
>
> Thank you very much.
>
>
> Yours sincerely
> Cheng
>
>
>
> All the screen output is below, quite long:
>
> --------------------------------------------------------------------------------------
> lanselibai at ubuntu:~/Cheng/gromacs/20170517_370K_paper1_mutants/HC_V215W$
> gmx pdb2gmx -f HC_V215W.pdb -o HC_V215W_processed.gro -water spce -inter
> -ignh -merge interactive
> GROMACS: gmx pdb2gmx, VERSION 5.0.4
>
> 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
>
> Copyright (c) 1991-2000, University of Groningen, The Netherlands.
> Copyright (c) 2001-2014, The GROMACS development team at
> Uppsala University, Stockholm University and
> the Royal Institute of Technology, Sweden.
> 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
> as published by the Free Software Foundation; either version 2.1
> of the License, or (at your option) any later version.
>
> GROMACS: gmx pdb2gmx, VERSION 5.0.4
> Executable: /usr/local/gromacs/bin/gmx
> Library dir: /usr/local/gromacs/share/gromacs/top
> Command line:
> gmx pdb2gmx -f HC_V215W.pdb -o HC_V215W_processed.gro -water spce -inter
> -ignh -merge interactive
>
>
> 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)
> 15
>
> Using the Oplsaa force field in directory oplsaa.ff
>
> Opening force field file
> /usr/local/gromacs/share/gromacs/top/oplsaa.ff/aminoacids.r2b
> Reading HC_V215W.pdb...
> Read 3342 atoms
> Analyzing pdb file
> Splitting chemical chains based on TER records or chain id changing.
> Merge chain ending with residue CYS214 (chain id 'L', atom 3258 SG) and
> chain starting with
> residue GLU215 (chain id 'H', atom 3263 N) into a single moleculetype
> (keeping termini)? [n/y]
> y
>
> Merged chains into joint molecule definitions at 1 places.
>
> There are 1 chains and 0 blocks of water and 442 residues with 3342 atoms
>
> chain #res #atoms
> 1 'L' 442 3342
>
> All occupancies are one
> Opening force field file
> /usr/local/gromacs/share/gromacs/top/oplsaa.ff/atomtypes.atp
> Atomtype 815
> Reading residue database... (oplsaa)
> Opening force field file
> /usr/local/gromacs/share/gromacs/top/oplsaa.ff/aminoacids.rtp
> Residue 54
> Sorting it all out...
> Opening force field file
> /usr/local/gromacs/share/gromacs/top/oplsaa.ff/aminoacids.hdb
> Opening force field file
> /usr/local/gromacs/share/gromacs/top/oplsaa.ff/aminoacids.n.tdb
> Opening force field file
> /usr/local/gromacs/share/gromacs/top/oplsaa.ff/aminoacids.c.tdb
> Processing chain 1 'L' (3342 atoms, 442 residues)
> Which LYSINE type do you want for residue 24
> 0. Not protonated (charge 0) (LYS)
> 1. Protonated (charge +1) (LYSH)
>
> Type a number:1
> Which LYSINE type do you want for residue 39
> 0. Not protonated (charge 0) (LYS)
> 1. Protonated (charge +1) (ARG)
>
> (here I just interactively assign protonation state)
>
> Identified residue ASP1 as a starting terminus.
> Identified residue CYS214 as a ending terminus.
> Identified residue GLU215 as a starting terminus.
> Identified residue ALA442 as a ending terminus.
> 8 out of 8 lines of specbond.dat converted successfully
> Special Atom Distance matrix:
> MET4 CYS23 HIS55 CYS88 HIS91 CYS134 HIS189
> SD31 SG163 NE2421 SG665 NE2692 SG1019 NE21459
> CYS23 SG163 0.484
> HIS55 NE2421 1.879 1.747
> CYS88 SG665 0.568 0.204 1.658
> HIS91 NE2692 1.038 1.094 0.947 1.019
> CYS134 SG1019 4.116 3.850 4.622 3.721 4.395
> HIS189 NE21459 5.014 4.894 5.848 4.778 5.416 1.796
> CYS194 SG1498 4.108 3.853 4.696 3.731 4.432 0.205 1.668
> HIS198 NE21531 3.366 3.002 3.877 2.909 3.707 1.340 2.965
> CYS214 SG1650 5.879 5.640 6.156 5.490 6.020 1.906 1.972
> CYS236 SG1801 2.365 2.395 1.426 2.237 1.490 4.436 5.369
> MET248 SD1888 2.082 2.169 1.125 2.051 1.117 4.798 5.746
> MET297 SD2276 2.679 2.880 2.988 2.735 2.453 4.071 4.366
> CYS310 SG2381 2.168 2.215 1.349 2.062 1.307 4.398 5.318
> CYS358 SG2707 4.527 4.269 4.383 4.088 4.407 1.720 2.803
> HIS382 NE22891 3.983 3.626 3.948 3.476 3.996 1.352 3.076
> CYS414 SG3121 4.596 4.343 4.374 4.158 4.428 1.936 2.977
> HIS418 NE23154 3.927 3.806 3.742 3.608 3.663 2.592 3.211
> CYS434 SG3284 5.939 5.703 6.166 5.548 6.048 2.022 2.098
> HIS438 NE23318 7.065 6.814 7.391 6.675 7.260 2.978 2.735
> CYS194 HIS198 CYS214 CYS236 MET248 MET297 CYS310
> SG1498 NE21531 SG1650 SG1801 SD1888 SD2276 SG2381
> HIS198 NE21531 1.371
> CYS214 SG1650 1.968 3.147
> CYS236 SG1801 4.515 4.101 5.705
> MET248 SD1888 4.863 4.327 6.187 0.629
> MET297 SD2276 4.089 4.159 5.182 1.863 2.140
> CYS310 SG2381 4.469 4.034 5.717 0.209 0.520 1.797
> CYS358 SG2707 1.902 2.454 1.985 3.900 4.417 3.804 3.944
> HIS382 NE22891 1.539 1.341 2.525 3.911 4.294 4.117 3.912
> CYS414 SG3121 2.117 2.633 2.117 3.853 4.385 3.795 3.907
> HIS418 NE23154 2.707 3.155 3.116 2.845 3.419 2.477 2.903
> CYS434 SG3284 2.096 3.257 0.203 5.683 6.178 5.171 5.702
> HIS438 NE23318 3.003 4.119 1.286 6.987 7.464 6.436 6.998
> CYS358 HIS382 CYS414 HIS418 CYS434
> SG2707 NE22891 SG3121 NE23154 SG3284
> HIS382 NE22891 1.328
> CYS414 SG3121 0.218 1.472
> HIS418 NE23154 1.514 2.397 1.441
> CYS434 SG3284 1.927 2.562 2.042 3.049
> HIS438 NE23318 3.206 3.607 3.321 4.379 1.331
> Link CYS-23 SG-163 and CYS-88 SG-665 (y/n) ?y
> Link CYS-134 SG-1019 and CYS-194 SG-1498 (y/n) ?y
> Link CYS-214 SG-1650 and CYS-434 SG-3284 (y/n) ?y
> Link CYS-236 SG-1801 and CYS-310 SG-2381 (y/n) ?y
> Link CYS-358 SG-2707 and CYS-414 SG-3121 (y/n) ?y
> Select start terminus type for ASP-1
> 0: NH3+
> 1: ZWITTERION_NH3+ (only use with zwitterions containing exactly one
> residue)
> 2: NH2
> 3: None
> 0
> Start terminus ASP-1: NH3+
> Select end terminus type for CYS-214
> 0: COO-
> 1: ZWITTERION_COO- (only use with zwitterions containing exactly one
> residue)
> 2: COOH
> 3: None
> 0
> End terminus CYS-214: COO-
> Select start terminus type for GLU-215
> 0: NH3+
> 1: ZWITTERION_NH3+ (only use with zwitterions containing exactly one
> residue)
> 2: NH2
> 3: None
> 0
> Start terminus GLU-215: NH3+
> Select end terminus type for ALA-442
> 0: COO-
> 1: ZWITTERION_COO- (only use with zwitterions containing exactly one
> residue)
> 2: COOH
> 3: None
> 2
> End terminus ALA-442: COOH
> Checking for duplicate atoms....
> Generating any missing hydrogen atoms and/or adding termini.
>
> -------------------------------------------------------
> Program gmx, VERSION 5.0.4
> Source code file:
> /home/lanselibai/Cheng/gromacs-5.0.4/src/gromacs/gmxpreprocess/pgutil.c,
> line: 125
>
> Fatal error:
> Residue 1 named ASP of a molecule in the input file was mapped
> to an entry in the topology database, but the atom N used in
> that entry is not found in the input file. Perhaps your atom
> and/or residue naming needs to be fixed.
>
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> -------------------------------------------------------
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