[gmx-users] pdb2gmx do not work for unstable conformations
ZHANG Cheng
272699575 at qq.com
Sat May 20 15:33:00 CEST 2017
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:
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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
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Per Larsson Justin A. Lemkul Magnus Lundborg Pieter Meulenhoff
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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
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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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