[gmx-users] Residue 1 mapping problem?
Justin Lemkul
jalemkul at vt.edu
Mon Aug 21 14:56:59 CEST 2017
On 8/21/17 6:20 AM, morpheus wrote:
> Hi,
>
> I would like to simulate chain D and E of pdb-id 1oga but pdb2gmx complains
> about the first (?) residues of the 2 chains:
>
> "WARNING: WARNING: Residue 1 named GLN of a molecule in the input file was
> mapped
> to an entry in the topology database, but the atom H used in
> an interaction of type angle in that entry is not found in the
> input file. Perhaps your atom and/or residue naming needs to be
> fixed."
This is an overly verbose message, which should not actually be a
"warning." Because you're requesting normal terminal patching (e.g.
NH3+), the H of residue 1 is deleted and will be replaced with H[123].
So this is really just telling you that's going on. It really shouldn't
be displayed, because it's confusing. But you receive no errors and you
can see that the topology was successfully generated.
-Justin
> I assume it means this GLN (as it is the first residue of the file):
>
> ATOM 3164 N GLN D 3 22.890 -35.428 -11.393 1.00
> 22.91 N
> ATOM 3165 CA GLN D 3 21.681 -35.958 -10.698 1.00
> 21.34 C
> ATOM 3166 C GLN D 3 20.599 -36.345 -11.695 1.00
> 20.99 C
> ATOM 3167 O GLN D 3 20.336 -35.616 -12.646 1.00
> 22.83 O
> ATOM 3168 CB GLN D 3 21.091 -34.889 -9.797 1.00
> 20.05 C
> ATOM 3169 CG GLN D 3 21.926 -34.493 -8.608 1.00
> 20.82 C
> ATOM 3170 CD GLN D 3 21.388 -33.220 -8.008 1.00
> 19.14 C
> ATOM 3171 OE1 GLN D 3 21.602 -32.139 -8.553 1.00
> 21.07 O
> ATOM 3172 NE2 GLN D 3 20.653 -33.341 -6.916 1.00
> 21.18 N
> ATOM 3173 N LEU D 4 19.949 -37.480 -11.445 1.00
> 21.46 N
> ATOM 3174 CA LEU D 4 18.889 -37.992 -12.300 1.00
> 22.61 C
> ATOM 3175 C LEU D 4 17.679 -38.428 -11.487 1.00
> 20.04 C
> ATOM 3176 O LEU D 4 17.814 -38.838 -10.337 1.00
> 21.78 O
> ATOM 3177 CB LEU D 4 19.386 -39.229 -13.059 1.00
> 22.96 C
> ATOM 3178 CG LEU D 4 20.637 -39.103 -13.912 1.00
> 26.17 C
> ATOM 3179 CD1 LEU D 4 21.062 -40.497 -14.412 1.00
> 29.25 C
> ATOM 3180 CD2 LEU D 4 20.341 -38.189 -15.071 1.00
> 27.56 C
>
> Any ideas? My commands and gromacs output below.
>
> Thanks!
>
>
>
> [b at localhost newTry]$ gmx pdb2gmx -f JM22_fullMHC_fullTCR.pdb -o
> JM22_fullMHC_fullTCR.gro -p JM22_fullMHC_fullTCR.top -i
> JM22_fullMHC_fullTCR.posre.itp -ignh -vsite hydrogens
> :-) GROMACS - gmx pdb2gmx, 2016.2 (-:
>
> GROMACS is written by:
> Emile Apol Rossen Apostolov Herman J.C. Berendsen Par
> Bjelkmar
> Aldert van Buuren Rudi van Drunen Anton Feenstra Gerrit Groenhof
> Christoph Junghans Anca Hamuraru Vincent Hindriksen Dimitrios
> Karkoulis
> Peter Kasson Jiri Kraus 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
> Teemu Virolainen 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) 2001-2015, 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 2016.2
> Executable: /usr/bin/gmx
> Data prefix: /usr
> Working dir:
> /home/b/data/projects/anton_mutationsMHC/complexes_withConstTcrRegions/JM22_onlyTCR/newTry
> Command line:
> gmx pdb2gmx -f JM22_fullMHC_fullTCR.pdb -o JM22_fullMHC_fullTCR.gro -p
> JM22_fullMHC_fullTCR.top -i JM22_fullMHC_fullTCR.posre.itp -ignh -vsite
> hydrogens
>
>
> Select the Force Field:
> From '/usr/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)
> 13
>
> Using the Gromos53a6 force field in directory gromos53a6.ff
>
> Opening force field file
> /usr/share/gromacs/top/gromos53a6.ff/watermodels.dat
>
> Select the Water Model:
> 1: SPC simple point charge, recommended
> 2: SPC/E extended simple point charge
> 3: None
> 1
> Opening force field file /usr/share/gromacs/top/gromos53a6.ff/aminoacids.r2b
> Reading JM22_fullMHC_fullTCR.pdb...
> Read 3462 atoms
> Analyzing pdb file
> Splitting chemical chains based on TER records or chain id changing.
> There are 2 chains and 0 blocks of water and 439 residues with 3462 atoms
>
> chain #res #atoms
> 1 'D' 199 1530
> 2 'E' 240 1932
>
> All occupancies are one
> Opening force field file /usr/share/gromacs/top/gromos53a6.ff/atomtypes.atp
> Atomtype 57
> Reading residue database... (gromos53a6)
> Opening force field file /usr/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/share/gromacs/top/gromos53a6.ff/aminoacids.hdb
> Opening force field file
> /usr/share/gromacs/top/gromos53a6.ff/aminoacids.n.tdb
> Opening force field file
> /usr/share/gromacs/top/gromos53a6.ff/aminoacids.c.tdb
> Processing chain 1 'D' (1530 atoms, 199 residues)
> Analysing hydrogen-bonding network for automated assignment of histidine
> protonation. 298 donors and 310 acceptors were found.
> There are 503 hydrogen bonds
> Will use HISE for residue 76
> Identified residue GLN3 as a starting terminus.
> Identified residue SER201 as a ending terminus.
> 8 out of 8 lines of specbond.dat converted successfully
> Special Atom Distance matrix:
> CYS24 HIS76 CYS90 CYS134 MET163 MET166
> SG177 NE2585 SG683 SG1003 SD1233 SD1258
> HIS76 NE2585 1.658
> CYS90 SG683 0.206 1.698
> CYS134 SG1003 4.473 4.152 4.315
> MET163 SD1233 3.926 3.135 3.791 2.051
> MET166 SD1258 4.251 3.327 4.126 2.367 0.458
> CYS184 SG1397 4.615 4.232 4.459 0.203 2.020 2.305
> Linking CYS-24 SG-177 and CYS-90 SG-683...
> Linking CYS-134 SG-1003 and CYS-184 SG-1397...
> Start terminus GLN-3: NH3+
> End terminus SER-201: COO-
> Checking for duplicate atoms....
> Generating any missing hydrogen atoms and/or adding termini.
> Now there are 199 residues with 1973 atoms
> Chain time...
> Making bonds...
> Number of bonds was 2010, now 2005
> Marked 442 virtual sites
> Added 28 dummy masses
> Added 85 new constraints
> Generating angles, dihedrals and pairs...
>
> WARNING: WARNING: Residue 1 named GLN of a molecule in the input file was
> mapped
> to an entry in the topology database, but the atom H used in
> an interaction of type angle in that entry is not found in the
> input file. Perhaps your atom and/or residue naming needs to be
> fixed.
>
>
>
> WARNING: WARNING: Residue 199 named SER of a molecule in the input file was
> mapped
> to an entry in the topology database, but the atom O used in
> an interaction of type angle in that entry is not found in the
> input file. Perhaps your atom and/or residue naming needs to be
> fixed.
>
>
> Before cleaning: 3265 pairs
> Before cleaning: 3814 dihedrals
> Making cmap torsions...
> There are 1067 dihedrals, 976 impropers, 2926 angles
> 3265 pairs, 2005 bonds and 413 virtual sites
> Total mass 21753.295 a.m.u.
> Total charge -4.000 e
> Writing topology
> Processing chain 2 'E' (1932 atoms, 240 residues)
> Analysing hydrogen-bonding network for automated assignment of histidine
> protonation. 385 donors and 375 acceptors were found.
> There are 613 hydrogen bonds
> Will use HISD for residue 31
> Will use HISE for residue 137
> Will use HISE for residue 154
> Will use HISE for residue 167
> Will use HISE for residue 207
> Identified residue GLY5 as a starting terminus.
> Identified residue ASP244 as a ending terminus.
> 8 out of 8 lines of specbond.dat converted successfully
> Special Atom Distance matrix:
> CYS25 HIS31 MET34 CYS93 HIS137 CYS145 HIS154
> SG165 NE2217 SD237 SG724 NE21067 SG1125 NE21197
> HIS31 NE2217 1.161
> MET34 SD237 0.420 0.902
> CYS93 SG724 0.202 1.161 0.334
> HIS137 NE21067 5.135 5.406 5.315 5.112
> CYS145 SG1125 3.301 3.963 3.619 3.334 2.514
> HIS154 NE21197 1.827 2.820 2.150 1.822 4.006 1.887
> HIS167 NE21309 2.618 2.926 2.885 2.688 3.033 1.490 2.132
> HIS207 NE21629 3.945 4.507 4.294 4.031 2.925 1.241 2.823
> CYS210 SG1657 3.201 3.842 3.524 3.244 2.597 0.203 1.871
> HIS167 HIS207
> NE21309 NE21629
> HIS207 NE21629 1.710
> CYS210 SG1657 1.313 1.139
> Linking CYS-25 SG-165 and CYS-93 SG-724...
> Linking CYS-145 SG-1125 and CYS-210 SG-1657...
> Start terminus GLY-5: GLY-NH3+
> End terminus ASP-244: COO-
> Checking for duplicate atoms....
> Generating any missing hydrogen atoms and/or adding termini.
> Now there are 240 residues with 2520 atoms
> Chain time...
> Making bonds...
> Number of bonds was 2580, now 2575
> Marked 587 virtual sites
> Added 24 dummy masses
> Added 87 new constraints
> Generating angles, dihedrals and pairs...
>
> WARNING: WARNING: Residue 1 named GLY of a molecule in the input file was
> mapped
> to an entry in the topology database, but the atom H used in
> an interaction of type angle in that entry is not found in the
> input file. Perhaps your atom and/or residue naming needs to be
> fixed.
>
>
>
> WARNING: WARNING: Residue 240 named ASP of a molecule in the input file was
> mapped
> to an entry in the topology database, but the atom O used in
> an interaction of type angle in that entry is not found in the
> input file. Perhaps your atom and/or residue naming needs to be
> fixed.
>
>
> Before cleaning: 4043 pairs
> Before cleaning: 4985 dihedrals
> Making cmap torsions...
> There are 1329 dihedrals, 1338 impropers, 3775 angles
> 4043 pairs, 2575 bonds and 548 virtual sites
> Total mass 27330.366 a.m.u.
> Total charge -4.000 e
> Writing topology
> Including chain 1 in system: 2001 atoms 199 residues
> Including chain 2 in system: 2544 atoms 240 residues
> Now there are 4545 atoms and 439 residues
> Total mass in system 49083.661 a.m.u.
> Total charge in system -8.000 e
>
> Writing coordinate file...
> --------- PLEASE NOTE ------------
> You have successfully generated a topology from: JM22_fullMHC_fullTCR.pdb.
> The Gromos53a6 force field and the spc water model are used.
> --------- ETON ESAELP ------------
>
> GROMACS reminds you: "You Could Make More Money As a Butcher" (F. Zappa)
>
> [b at localhost newTry]$
--
==================================================
Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry
303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061
jalemkul at vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
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