[gmx-users] Fix the residues
Justin Lemkul
jalemkul at vt.edu
Fri Jan 6 21:04:55 CET 2017
On 1/6/17 2:41 PM, liming_52 wrote:
> Thank you for reppy. The full information is as follows:
> $ gmx pdb2gmx -f lactoferrin.pdb -o lactoferrin.gro -water spce
> :-) GROMACS - gmx pdb2gmx, VERSION 5.1.4 (-:
> 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 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 5.1.4
> Executable: /usr/local/gromacs/bin//gmx.exe
> Data prefix: /usr/local/gromacs
> Command line:
> gmx pdb2gmx -f lactoferrin.pdb -o lactoferrin.gro -water spce
>
> 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)
> 9
> Using the Gromos43a1 force field in directory gromos43a1.ff
> Opening force field file /usr/local/gromacs/share/gromacs/top/gromos43a1.ff/aminoacids.r2b
> Reading lactoferrin.pdb...
> WARNING: all CONECT records are ignored
> Read 2560 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 335 residues with 2560 atoms
> chain #res #atoms
> 1 'A' 335 2560
> All occupancies are one
> Opening force field file /usr/local/gromacs/share/gromacs/top/gromos43a1.ff/atomtypes.atp
> Atomtype 50
> Reading residue database... (gromos43a1)
> Opening force field file /usr/local/gromacs/share/gromacs/top/gromos43a1.ff/aminoacids.rtp
> Residue 96
> Sorting it all out...
> Opening force field file /usr/local/gromacs/share/gromacs/top/gromos43a1.ff/aminoacids.hdb
> Opening force field file /usr/local/gromacs/share/gromacs/top/gromos43a1.ff/aminoacids.n.tdb
> Opening force field file /usr/local/gromacs/share/gromacs/top/gromos43a1.ff/aminoacids.c.tdb
> Back Off! I just backed up topol.top to ./#topol.top.1#
> Processing chain 1 'A' (2560 atoms, 335 residues)
> Analysing hydrogen-bonding network for automated assignment of histidine
> protonation. 500 donors and 499 acceptors were found.
> There are 743 hydrogen bonds
> Will use HISE for residue 420
> Will use HISH for residue 458
> Will use HISD for residue 588
> Will use HISE for residue 595
> Will use HISE for residue 606
> Will use HISE for residue 613
> Identified residue TYR342 as a starting terminus.
> Identified residue SER676 as a ending terminus.
> 8 out of 8 lines of specbond.dat converted successfully
> Special Atom Distance matrix:
> CYS348 CYS358 CYS371 CYS380 CYS405 HIS420 CYS425
> SG64 SG138 SG241 SG300 SG481 NE2595 SG629
> CYS358 SG138 0.849
> CYS371 SG241 0.940 0.213
> CYS380 SG300 0.204 0.933 1.049
> CYS405 SG481 1.411 2.186 2.303 1.371
> HIS420 NE2595 3.406 3.321 3.509 3.348 3.338
> CYS425 SG629 2.460 2.150 2.323 2.429 2.901 1.313
> CYS457 SG875 2.702 2.932 3.096 2.502 2.930 3.532 3.094
> HIS458 NE2885 2.548 2.968 3.141 2.345 2.426 3.418 3.123
> MET471 SD983 2.682 3.182 3.361 2.487 2.293 3.347 3.207
> CYS481 SG1051 3.086 3.770 3.933 2.924 2.167 3.844 3.883
> CYS491 SG1133 2.184 2.509 2.651 1.985 2.495 3.728 3.130
> CYS502 SG1209 2.159 2.671 2.793 1.969 2.249 4.093 3.530
> CYS505 SG1228 2.166 2.539 2.672 1.970 2.452 3.880 3.273
> CYS515 SG1297 2.029 2.503 2.628 1.837 2.216 3.962 3.362
> CYS532 SG1436 2.629 2.850 3.005 2.431 2.930 3.653 3.146
> CYS573 SG1764 3.775 3.952 4.158 3.598 3.597 2.648 2.951
> CYS587 SG1867 3.594 3.755 3.960 3.419 3.463 2.533 2.771
> HIS588 NE21877 3.277 3.459 3.671 3.127 3.007 1.800 2.233
> HIS595 NE21927 1.637 1.836 2.046 1.488 1.825 2.179 1.605
> HIS606 NE22008 1.686 1.478 1.480 1.846 2.316 3.172 2.230
> HIS613 NE22066 2.250 1.623 1.635 2.359 3.154 2.929 1.780
> CYS625 SG2156 2.333 1.651 1.753 2.329 3.350 2.606 1.332
> CYS630 SG2197 2.270 1.572 1.667 2.261 3.342 2.763 1.491
> CYS647 SG2337 2.306 2.002 2.173 2.286 2.760 1.421 0.205
> CYS675 SG2554 2.907 3.577 3.743 2.742 2.024 3.670 3.679
> CYS457 HIS458 MET471 CYS481 CYS491 CYS502 CYS505
> SG875 NE2885 SD983 SG1051 SG1133 SG1209 SG1228
> HIS458 NE2885 0.746
> MET471 SD983 1.209 0.486
> CYS481 SG1051 2.332 1.591 1.152
> CYS491 SG1133 0.700 0.843 1.287 2.240
> CYS502 SG1209 1.263 1.036 1.308 1.939 0.670
> CYS505 SG1228 0.873 0.919 1.329 2.200 0.207 0.484
> CYS515 SG1297 1.171 1.014 1.329 2.039 0.523 0.202 0.343
> CYS532 SG1436 0.207 0.847 1.329 2.423 0.569 1.166 0.740
> CYS573 SG1764 1.883 1.857 1.818 2.626 2.461 2.877 2.626
> CYS587 SG1867 1.757 1.754 1.744 2.603 2.323 2.759 2.493
> HIS588 NE21877 2.175 1.985 1.862 2.508 2.559 2.918 2.715
> HIS595 NE21927 1.755 1.601 1.689 2.421 1.670 1.978 1.789
> HIS606 NE22008 4.076 3.936 3.996 4.306 3.707 3.784 3.737
> HIS613 NE22066 4.109 4.155 4.299 4.857 3.868 4.130 3.948
> CYS625 SG2156 3.130 3.389 3.640 4.482 3.059 3.515 3.190
> CYS630 SG2197 3.034 3.320 3.592 4.455 2.945 3.405 3.073
> CYS647 SG2337 3.121 3.125 3.204 3.846 3.112 3.483 3.246
> CYS675 SG2554 2.186 1.441 1.001 0.209 2.089 1.817 2.058
> CYS515 CYS532 CYS573 CYS587 HIS588 HIS595 HIS606
> SG1297 SG1436 SG1764 SG1867 NE21877 NE21927 NE22008
> CYS532 SG1436 1.063
> CYS573 SG1764 2.816 2.085
> CYS587 SG1867 2.687 1.956 0.205
> HIS588 NE21877 2.835 2.354 0.952 0.859
> HIS595 NE21927 1.831 1.805 2.198 2.012 1.663
> HIS606 NE22008 3.645 4.043 4.641 4.457 3.901 2.523
> HIS613 NE22066 3.956 4.078 4.559 4.364 3.878 2.644 1.163
> CYS625 SG2156 3.318 3.104 3.598 3.398 3.138 2.074 2.269
> CYS630 SG2197 3.206 2.996 3.606 3.404 3.187 2.069 2.325
> CYS647 SG2337 3.316 3.165 3.060 2.878 2.325 1.567 2.028
> CYS675 SG2554 1.902 2.278 2.507 2.470 2.354 2.213 4.124
> HIS613 CYS625 CYS630 CYS647
> NE22066 SG2156 SG2197 SG2337
> CYS625 SG2156 1.454
> CYS630 SG2197 1.554 0.210
> CYS647 SG2337 1.628 1.318 1.473
> CYS675 SG2554 4.656 4.273 4.247 3.642
> Linking CYS-348 SG-64 and CYS-380 SG-300...
> Linking CYS-358 SG-138 and CYS-371 SG-241...
> Linking CYS-425 SG-629 and CYS-647 SG-2337...
> Linking CYS-457 SG-875 and CYS-532 SG-1436...
> Linking CYS-481 SG-1051 and CYS-675 SG-2554...
> Linking CYS-491 SG-1133 and CYS-505 SG-1228...
> Linking CYS-502 SG-1209 and CYS-515 SG-1297...
> Linking CYS-573 SG-1764 and CYS-587 SG-1867...
> Linking CYS-625 SG-2156 and CYS-630 SG-2197...
> Start terminus TYR-342: NH3+
> End terminus SER-676: COO-
> Checking for duplicate atoms....
> Generating any missing hydrogen atoms and/or adding termini.
> Now there are 335 residues with 3278 atoms
> Making bonds...
> Number of bonds was 3340, now 3335
> Generating angles, dihedrals and pairs...
> WARNING: WARNING: Residue 1 named TYR 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 335 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: 5477 pairs
> Before cleaning: 6310 dihedrals
> Making cmap torsions...
> There are 1781 dihedrals, 1618 impropers, 4878 angles
> 5477 pairs, 3335 bonds and 0 virtual sites
> Total mass 36559.344 a.m.u.
> Total charge 0.000 e
> Writing topology
> Back Off! I just backed up posre.itp to ./#posre.itp.1#
> Writing coordinate file...
> Back Off! I just backed up lactoferrin.gro to ./#lactoferrin.gro.1#
> --------- PLEASE NOTE ------------
> You have successfully generated a topology from: lactoferrin.pdb.
> The Gromos43a1 force field and the spce water model are used.
> --------- ETON ESAELP ------------
> gcq#395: "It was something to at least have a choice of nightmares" (Joseph Conrad)
>
And this indicates that nothing is wrong.
The WARNING messages above shouldn't show up under normal usage unless maybe
you've compiled with debugging symbols on (I thought that only came up with -v
or maybe with -missing) but it just means your residues are being patched via
the normal .tdb mechanisms.
-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
==================================================
More information about the gromacs.org_gmx-users
mailing list