:-) GROMACS - gmx pdb2gmx, 2020.2 (-: GROMACS is written by: Emile Apol Rossen Apostolov Paul Bauer Herman J.C. Berendsen Par Bjelkmar Christian Blau Viacheslav Bolnykh Kevin Boyd Aldert van Buuren Rudi van Drunen Anton Feenstra Alan Gray Gerrit Groenhof Anca Hamuraru Vincent Hindriksen M. Eric Irrgang Aleksei Iupinov Christoph Junghans Joe Jordan Dimitrios Karkoulis Peter Kasson Jiri Kraus Carsten Kutzner Per Larsson Justin A. Lemkul Viveca Lindahl Magnus Lundborg Erik Marklund Pascal Merz Pieter Meulenhoff Teemu Murtola Szilard Pall Sander Pronk Roland Schulz Michael Shirts Alexey Shvetsov Alfons Sijbers Peter Tieleman Jon Vincent Teemu Virolainen Christian Wennberg Maarten Wolf Artem Zhmurov 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) 2001-2019, 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 2020.2 Executable: /usr/local/tools/_conda/envs/__gromacs@2020.2/bin.AVX2_256/gmx Data prefix: /usr/local/tools/_conda/envs/__gromacs@2020.2 Working dir: /data/jwd02f/main/075/054/75054916/working Command line: gmx pdb2gmx -f ./pdb_input.pdb -o processed.gro -p topol.top -i posres.itp -water spce -ff oplsaa -noignh -merge all Opening force field file /usr/local/tools/_conda/envs/__gromacs@2020.2/share/gromacs/top/oplsaa.ff/aminoacids.r2b WARNING: all CONECT records are ignored All occupancies are one Opening force field file /usr/local/tools/_conda/envs/__gromacs@2020.2/share/gromacs/top/oplsaa.ff/atomtypes.atp Opening force field file /usr/local/tools/_conda/envs/__gromacs@2020.2/share/gromacs/top/oplsaa.ff/aminoacids.rtp Opening force field file /usr/local/tools/_conda/envs/__gromacs@2020.2/share/gromacs/top/oplsaa.ff/aminoacids.hdb Opening force field file /usr/local/tools/_conda/envs/__gromacs@2020.2/share/gromacs/top/oplsaa.ff/aminoacids.n.tdb Opening force field file /usr/local/tools/_conda/envs/__gromacs@2020.2/share/gromacs/top/oplsaa.ff/aminoacids.c.tdb Analysing hydrogen-bonding network for automated assignment of histidine protonation. 213 donors and 184 acceptors were found. There are 255 hydrogen bonds Will use HISE for residue 15 8 out of 8 lines of specbond.dat converted successfully Special Atom Distance matrix: CYS6 MET12 HIS15 CYS30 CYS64 CYS76 CYS80 SG48 SD87 NE2118 SG238 SG513 SG601 SG630 MET12 SD87 1.166 HIS15 NE2118 1.776 1.019 CYS30 SG238 1.406 1.054 2.069 CYS64 SG513 2.835 1.794 1.789 2.241 CYS76 SG601 2.704 1.551 1.468 2.116 0.765 CYS80 SG630 2.959 1.951 1.916 2.391 0.199 0.944 CYS94 SG724 2.550 1.407 1.382 1.975 0.665 0.202 0.855 MET105 SD799 1.827 0.911 1.683 0.888 1.849 1.461 2.036 CYS115 SG889 1.576 1.084 2.078 0.200 2.111 1.989 2.262 CYS127 SG981 0.197 1.072 1.721 1.313 2.799 2.622 2.934 CYS94 MET105 CYS115 SG724 SD799 SG889 MET105 SD799 1.381 CYS115 SG889 1.853 0.790 CYS127 SG981 2.475 1.686 1.483 Linking CYS-6 SG-48 and CYS-127 SG-981... Linking CYS-30 SG-238 and CYS-115 SG-889... Linking CYS-64 SG-513 and CYS-80 SG-630... Linking CYS-76 SG-601 and CYS-94 SG-724... Making bonds... Number of bonds was 1984, now 1984 Generating angles, dihedrals and pairs... Before cleaning: 5142 pairs Before cleaning: 5187 dihedrals Keeping all generated dihedrals Making cmap torsions... There are 5187 dihedrals, 426 impropers, 3547 angles 5106 pairs, 1984 bonds and 0 virtual sites Total mass 14313.193 a.m.u. Total charge 8.000 e Writing topology Writing coordinate file... GROMACS reminds you: "Is That a Real Poncho ?" (F. Zappa) Using the Oplsaa force field in directory oplsaa.ff going to rename oplsaa.ff/aminoacids.r2b Reading ./pdb_input.pdb... Read 'LYSOZYME', 1001 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 129 residues with 1001 atoms chain #res #atoms 1 'A' 129 1001 Reading residue database... (Oplsaa) Processing chain 1 'A' (1001 atoms, 129 residues) Identified residue LYS1 as a starting terminus. Identified residue LEU129 as a ending terminus. Start terminus LYS-1: NH3+ End terminus LEU-129: COO- Checking for duplicate atoms.... Generating any missing hydrogen atoms and/or adding termini. Now there are 129 residues with 1960 atoms --------- PLEASE NOTE ------------ You have successfully generated a topology from: ./pdb_input.pdb. The Oplsaa force field and the spce water model are used. --------- ETON ESAELP ------------