[gmx-users] gromacs warning topology file naming residues
Justin Lemkul
jalemkul at vt.edu
Thu May 5 13:59:59 CEST 2016
On 5/5/16 7:58 AM, Upasana Ray wrote:
> pdb2gmx -f receptor.pdb -o recep.gro -p recep.top -i recep.itp
> GROMACS: gmx pdb2gmx, VERSION 5.0.7
>
> 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 5.0.7
> Executable: /usr/local/gromacs/bin/gmx
> Library dir: /usr/local/gromacs/share/gromacs/top
> Command line:
> pdb2gmx -f receptor.pdb -o recep.gro -p recep.top -i recep.itp
>
>
> 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)
> 13
>
> Using the Gromos53a6 force field in directory gromos53a6.ff
>
> Opening force field file
> /usr/local/gromacs/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/local/gromacs/share/gromacs/top/gromos53a6.ff/aminoacids.r2b
> Reading receptor.pdb...
> Read 2712 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 318 residues with 2712 atoms
>
> chain #res #atoms
> 1 ' ' 318 2712
>
> 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
>
> Back Off! I just backed up recep.top to ./#recep.top.6#
> Processing chain 1 (2712 atoms, 318 residues)
> Analysing hydrogen-bonding network for automated assignment of histidine
> protonation. 476 donors and 475 acceptors were found.
> There are 712 hydrogen bonds
> Will use HISE for residue 148
> Will use HISE for residue 179
> Identified residue MET1 as a starting terminus.
> Identified residue ASP318 as a ending terminus.
> 8 out of 8 lines of specbond.dat converted successfully
> Special Atom Distance matrix:
> MET1 MET18 CYS36 CYS44 MET49 CYS60 CYS94
> SD8 SD144 SG292 SG356 SD397 SG492 SG794
> MET18 SD144 1.598
> CYS36 SG292 6.667 5.296
> CYS44 SG356 8.837 7.478 2.301
> MET49 SD397 10.320 8.864 3.717 2.019
> CYS60 SG492 13.450 11.986 6.872 4.783 3.248
> CYS94 SG794 20.844 19.314 14.849 12.884 11.492 8.577
> CYS99 SG841 22.213 20.670 16.284 14.366 12.923 10.043 1.579
> HIS148 NE21277 23.143 21.630 17.270 15.289 13.987 11.063 2.579
> HIS179 NE21548 24.321 22.789 18.768 16.961 15.616 12.926 4.556
> MET181 SD1563 23.994 22.477 18.367 16.490 15.207 12.443 3.998
> MET214 SD1855 21.702 20.197 16.275 14.484 13.302 10.765 3.263
> MET235 SD2024 24.164 22.667 18.421 16.451 15.230 12.351 3.974
> MET248 SD2135 24.492 23.027 19.098 17.218 16.146 13.471 5.495
> CYS249 SG2143 24.861 23.398 19.596 17.768 16.707 14.109 6.178
> MET287 SD2464 21.466 20.208 15.629 13.392 12.875 10.149 7.761
> MET297 SD2547 21.781 20.638 15.983 13.755 13.447 10.951 10.338
> CYS99 HIS148 HIS179 MET181 MET214 MET235 MET248
> SG841 NE21277 NE21548 SD1563 SD1855 SD2024 SD2135
> HIS148 NE21277 1.732
> HIS179 NE21548 3.220 2.776
> MET181 SD1563 2.836 1.878 1.129
> MET214 SD1855 2.963 2.777 2.881 2.451
> MET235 SD2024 3.082 1.461 2.444 1.367 3.057
> MET248 SD2135 4.758 3.374 2.938 2.246 3.206 2.139
> CYS249 SG2143 5.371 4.119 3.093 2.703 3.584 2.906 0.891
> MET287 SD2464 8.760 8.018 10.596 9.499 9.043 8.375 9.193
> MET297 SD2547 11.405 10.810 13.480 12.399 11.992 11.253 12.199
> CYS249 MET287
> SG2143 SD2464
> MET287 SD2464 10.006
> MET297 SD2547 13.024 3.061
> Start terminus MET-1: NH3+
> End terminus ASP-318: COO-
> Checking for duplicate atoms....
> Generating any missing hydrogen atoms and/or adding termini.
> Now there are 318 residues with 3025 atoms
> Making bonds...
> Number of bonds was 3063, now 3058
> Generating angles, dihedrals and pairs...
>
> WARNING: WARNING: Residue 1 named MET 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 318 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: 5315 pairs
> Before cleaning: 5784 dihedrals
> Making cmap torsions...
> There are 1702 dihedrals, 1403 impropers, 4425 angles
> 5315 pairs, 3058 bonds and 0 virtual sites
> Total mass 34482.681 a.m.u.
> Total charge -8.000 e
> Writing topology
>
> Back Off! I just backed up recep.itp to ./#recep.itp.2#
>
> Writing coordinate file...
>
> Back Off! I just backed up recep.gro to ./#recep.gro.2#
> --------- PLEASE NOTE ------------
> You have successfully generated a topology from: receptor.pdb.
> The Gromos53a6 force field and the spc water model are used.
> --------- ETON ESAELP ------------
>
> gcq#139: "One Ripple At a Time" (Bianca's Smut Shack)
>
OK, so everything is fine. I don't know why the warnings are printed, but
there's not actually a problem here.
-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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