$ gmx pdb2gmx -f protein.pdb -o protein_processed.gro -water tip3p -inter -ignh -merge interactive :-) GROMACS - gmx pdb2gmx, 2021 (-: GROMACS is written by: Andrey Alekseenko 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 Gilles Gouaillardet 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 2021 Executable: /usr/local/gromacs/bin/gmx Data prefix: /usr/local/gromacs Working dir: /mnt/c/Users/james/Downloads/test Command line: gmx pdb2gmx -f protein.pdb -o protein_processed.gro -water tip3p -inter -ignh -merge interactive Select the Force Field: From '/usr/local/gromacs/share/gromacs/top': 1: amber14sb.ff 2: AMBER03 protein, nucleic AMBER94 (Duan et al., J. Comp. Chem. 24, 1999-2012, 2003) 3: AMBER94 force field (Cornell et al., JACS 117, 5179-5197, 1995) 4: AMBER96 protein, nucleic AMBER94 (Kollman et al., Acc. Chem. Res. 29, 461-469, 1996) 5: AMBER99 protein, nucleic AMBER94 (Wang et al., J. Comp. Chem. 21, 1049-1074, 2000) 6: AMBER99SB protein, nucleic AMBER94 (Hornak et al., Proteins 65, 712-725, 2006) 7: AMBER99SB-ILDN protein, nucleic AMBER94 (Lindorff-Larsen et al., Proteins 78, 1950-58, 2010) 8: AMBERGS force field (Garcia & Sanbonmatsu, PNAS 99, 2782-2787, 2002) 9: CHARMM27 all-atom force field (CHARM22 plus CMAP for proteins) 10: GROMOS96 43a1 force field 11: GROMOS96 43a2 force field (improved alkane dihedrals) 12: GROMOS96 45a3 force field (Schuler JCC 2001 22 1205) 13: GROMOS96 53a5 force field (JCC 2004 vol 25 pag 1656) 14: GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656) 15: GROMOS96 54a7 force field (Eur. Biophys. J. (2011), 40,, 843-856, DOI: 10.1007/s00249-011-0700-9) 16: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals) 16 Using the Oplsaa force field in directory oplsaa.ff going to rename oplsaa.ff/aminoacids.r2b Opening force field file /usr/local/gromacs/share/gromacs/top/oplsaa.ff/aminoacids.r2b Reading protein.pdb... Read '', 3336 atoms Analyzing pdb file Splitting chemical chains based on TER records or chain id changing. Merge chain ending with residue CYS214 (chain id 'A', atom 3258 SG) and chain starting with residue GLU215 (chain id 'B', atom 3264 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 3336 atoms chain #res #atoms 1 'A' 442 3336 All occupancies are one All occupancies are one Opening force field file /usr/local/gromacs/share/gromacs/top/oplsaa.ff/atomtypes.atp Reading residue database... (Oplsaa) Opening force field file /usr/local/gromacs/share/gromacs/top/oplsaa.ff/aminoacids.rtp 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 'A' (3336 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) (LYSH) Type a number:1 Which LYSINE type do you want for residue 42 0. Not protonated (charge 0) (LYS) 1. Protonated (charge +1) (LYSH) Type a number:1 Which LYSINE type do you want for residue 45 0. Not protonated (charge 0) (LYS) 1. Protonated (charge +1) (LYSH) Type a number:0 Which LYSINE type do you want for residue 103 0. Not protonated (charge 0) (LYS) 1. Protonated (charge +1) (LYSH) Type a number:1 Which LYSINE type do you want for residue 107 0. Not protonated (charge 0) (LYS) 1. Protonated (charge +1) (LYSH) Type a number:1 Which LYSINE type do you want for residue 126 0. Not protonated (charge 0) (LYS) 1. Protonated (charge +1) (LYSH) Type a number:1 Which LYSINE type do you want for residue 145 0. Not protonated (charge 0) (LYS) 1. Protonated (charge +1) (LYSH) Type a number:1 Which LYSINE type do you want for residue 149 0. Not protonated (charge 0) (LYS) 1. Protonated (charge +1) (LYSH) Type a number:1 Which LYSINE type do you want for residue 169 0. Not protonated (charge 0) (LYS) 1. Protonated (charge +1) (LYSH) Type a number:1 Which LYSINE type do you want for residue 183 0. Not protonated (charge 0) (LYS) 1. Protonated (charge +1) (LYSH) Type a number:1 Which LYSINE type do you want for residue 188 0. Not protonated (charge 0) (LYS) 1. Protonated (charge +1) (LYSH) Type a number:1 Which LYSINE type do you want for residue 190 0. Not protonated (charge 0) (LYS) 1. Protonated (charge +1) (LYSH) Type a number:1 Which LYSINE type do you want for residue 207 0. Not protonated (charge 0) (LYS) 1. Protonated (charge +1) (LYSH) Type a number:1 Which LYSINE type do you want for residue 257 0. Not protonated (charge 0) (LYS) 1. Protonated (charge +1) (LYSH) Type a number:1 Which LYSINE type do you want for residue 279 0. Not protonated (charge 0) (LYS) 1. Protonated (charge +1) (LYSH) Type a number:1 Which LYSINE type do you want for residue 290 0. Not protonated (charge 0) (LYS) 1. Protonated (charge +1) (LYSH) Type a number:1 Which LYSINE type do you want for residue 335 0. Not protonated (charge 0) (LYS) 1. Protonated (charge +1) (LYSH) Type a number:1 Which LYSINE type do you want for residue 347 0. Not protonated (charge 0) (LYS) 1. Protonated (charge +1) (LYSH) Type a number:1 Which LYSINE type do you want for residue 361 0. Not protonated (charge 0) (LYS) 1. Protonated (charge +1) (LYSH) Type a number:1 Which LYSINE type do you want for residue 419 0. Not protonated (charge 0) (LYS) 1. Protonated (charge +1) (LYSH) Type a number:1 Which LYSINE type do you want for residue 424 0. Not protonated (charge 0) (LYS) 1. Protonated (charge +1) (LYSH) Type a number:1 Which LYSINE type do you want for residue 427 0. Not protonated (charge 0) (LYS) 1. Protonated (charge +1) (LYSH) Type a number:1 Which LYSINE type do you want for residue 428 0. Not protonated (charge 0) (LYS) 1. Protonated (charge +1) (LYSH) Type a number:1 Which LYSINE type do you want for residue 432 0. Not protonated (charge 0) (LYS) 1. Protonated (charge +1) (LYSH) Type a number:1 Which LYSINE type do you want for residue 436 0. Not protonated (charge 0) (LYS) 1. Protonated (charge +1) (LYSH) Type a number:1 Which ARGININE type do you want for residue 18 0. Not protonated (charge 0) (ARGN) 1. Protonated (charge +1) (ARG) Type a number:1 Which ARGININE type do you want for residue 30 0. Not protonated (charge 0) (ARGN) 1. Protonated (charge +1) (ARG) Type a number:1 Which ARGININE type do you want for residue 54 0. Not protonated (charge 0) (ARGN) 1. Protonated (charge +1) (ARG) Type a number:1 Which ARGININE type do you want for residue 61 0. Not protonated (charge 0) (ARGN) 1. Protonated (charge +1) (ARG) Type a number:1 Which ARGININE type do you want for residue 108 0. Not protonated (charge 0) (ARGN) 1. Protonated (charge +1) (ARG) Type a number:1 Which ARGININE type do you want for residue 142 0. Not protonated (charge 0) (ARGN) 1. Protonated (charge +1) (ARG) Type a number:1 Which ARGININE type do you want for residue 211 0. Not protonated (charge 0) (ARGN) 1. Protonated (charge +1) (ARG) Type a number:1 Which ARGININE type do you want for residue 233 0. Not protonated (charge 0) (ARGN) 1. Protonated (charge +1) (ARG) Type a number:1 Which ARGININE type do you want for residue 252 0. Not protonated (charge 0) (ARGN) 1. Protonated (charge +1) (ARG) Type a number:1 Which ARGININE type do you want for residue 281 0. Not protonated (charge 0) (ARGN) 1. Protonated (charge +1) (ARG) Type a number:1 Which ARGININE type do you want for residue 286 0. Not protonated (charge 0) (ARGN) 1. Protonated (charge +1) (ARG) Type a number:1 Which ARGININE type do you want for residue 301 0. Not protonated (charge 0) (ARGN) 1. Protonated (charge +1) (ARG) Type a number:1 Which GLUTAMINE type do you want for residue 3 0. Not protonated (charge 0) (GLN) 1. Protonated (charge +1) (QLN) Type a number:0 Which GLUTAMINE type do you want for residue 6 0. Not protonated (charge 0) (GLN) 1. Protonated (charge +1) (QLN) Type a number:0 Which GLUTAMINE type do you want for residue 27 0. Not protonated (charge 0) (GLN) 1. Protonated (charge +1) (QLN) Type a number:0 Which GLUTAMINE type do you want for residue 37 0. Not protonated (charge 0) (GLN) 1. Protonated (charge +1) (QLN) Type a number:0 Which GLUTAMINE type do you want for residue 38 0. Not protonated (charge 0) (GLN) 1. Protonated (charge +1) (QLN) Type a number:0 Which GLUTAMINE type do you want for residue 79 0. Not protonated (charge 0) (GLN) 1. Protonated (charge +1) (QLN) Type a number:0 Which GLUTAMINE type do you want for residue 90 0. Not protonated (charge 0) (GLN) 1. Protonated (charge +1) (QLN) Type a number:0 Which GLUTAMINE type do you want for residue 100 0. Not protonated (charge 0) (GLN) 1. Protonated (charge +1) (QLN) Type a number:0 Which GLUTAMINE type do you want for residue 124 0. Not protonated (charge 0) (GLN) 1. Protonated (charge +1) (QLN) Type a number:0 Which GLUTAMINE type do you want for residue 147 0. Not protonated (charge 0) (GLN) 1. Protonated (charge +1) (QLN) Type a number:0 Which GLUTAMINE type do you want for residue 155 0. Not protonated (charge 0) (GLN) 1. Protonated (charge +1) (QLN) Type a number:0 Which GLUTAMINE type do you want for residue 160 0. Not protonated (charge 0) (GLN) 1. Protonated (charge +1) (QLN) Type a number:0 Which GLUTAMINE type do you want for residue 166 0. Not protonated (charge 0) (GLN) 1. Protonated (charge +1) (QLN) Type a number:0 Which GLUTAMINE type do you want for residue 199 0. Not protonated (charge 0) (GLN) 1. Protonated (charge +1) (QLN) Type a number:0 Which GLUTAMINE type do you want for residue 217 0. Not protonated (charge 0) (GLN) 1. Protonated (charge +1) (QLN) Type a number:0 Which GLUTAMINE type do you want for residue 227 0. Not protonated (charge 0) (GLN) 1. Protonated (charge +1) (QLN) Type a number:0 Which GLUTAMINE type do you want for residue 253 0. Not protonated (charge 0) (GLN) 1. Protonated (charge +1) (QLN) Type a number:0 Which GLUTAMINE type do you want for residue 296 0. Not protonated (charge 0) (GLN) 1. Protonated (charge +1) (QLN) Type a number:0 Which GLUTAMINE type do you want for residue 323 0. Not protonated (charge 0) (GLN) 1. Protonated (charge +1) (QLN) Type a number:0 Which GLUTAMINE type do you want for residue 389 0. Not protonated (charge 0) (GLN) 1. Protonated (charge +1) (QLN) Type a number:0 Which GLUTAMINE type do you want for residue 410 0. Not protonated (charge 0) (GLN) 1. Protonated (charge +1) (QLN) Type a number:0 Which ASPARTIC ACID type do you want for residue 1 0. Not protonated (charge -1) (ASP) 1. Protonated (charge 0) (ASPH) Type a number:0 Which ASPARTIC ACID type do you want for residue 17 0. Not protonated (charge -1) (ASP) 1. Protonated (charge 0) (ASPH) Type a number:0 Which ASPARTIC ACID type do you want for residue 70 0. Not protonated (charge -1) (ASP) 1. Protonated (charge 0) (ASPH) Type a number:0 Which ASPARTIC ACID type do you want for residue 82 0. Not protonated (charge -1) (ASP) 1. Protonated (charge 0) (ASPH) Type a number:0 Which ASPARTIC ACID type do you want for residue 122 0. Not protonated (charge -1) (ASP) 1. Protonated (charge 0) (ASPH) Type a number:0 Which ASPARTIC ACID type do you want for residue 151 0. Not protonated (charge -1) (ASP) 1. Protonated (charge 0) (ASPH) Type a number:0 Which ASPARTIC ACID type do you want for residue 167 0. Not protonated (charge -1) (ASP) 1. Protonated (charge 0) (ASPH) Type a number:0 Which ASPARTIC ACID type do you want for residue 170 0. Not protonated (charge -1) (ASP) 1. Protonated (charge 0) (ASPH) Type a number:0 Which ASPARTIC ACID type do you want for residue 185 0. Not protonated (charge -1) (ASP) 1. Protonated (charge 0) (ASPH) Type a number:0 Which ASPARTIC ACID type do you want for residue 247 0. Not protonated (charge -1) (ASP) 1. Protonated (charge 0) (ASPH) Type a number:0 Which ASPARTIC ACID type do you want for residue 276 0. Not protonated (charge -1) (ASP) 1. Protonated (charge 0) (ASPH) Type a number:0 Which ASPARTIC ACID type do you want for residue 287 0. Not protonated (charge -1) (ASP) 1. Protonated (charge 0) (ASPH) Type a number:0 Which ASPARTIC ACID type do you want for residue 304 0. Not protonated (charge -1) (ASP) 1. Protonated (charge 0) (ASPH) Type a number:0 Which ASPARTIC ACID type do you want for residue 362 0. Not protonated (charge -1) (ASP) 1. Protonated (charge 0) (ASPH) Type a number:0 Which ASPARTIC ACID type do you want for residue 426 0. Not protonated (charge -1) (ASP) 1. Protonated (charge 0) (ASPH) Type a number:0 Which ASPARTIC ACID type do you want for residue 435 0. Not protonated (charge -1) (ASP) 1. Protonated (charge 0) (ASPH) Type a number:0 Which GLUTAMIC ACID type do you want for residue 81 0. Not protonated (charge -1) (GLU) 1. Protonated (charge 0) (GLUH) Type a number:0 Which GLUTAMIC ACID type do you want for residue 105 0. Not protonated (charge -1) (GLU) 1. Protonated (charge 0) (GLUH) Type a number:0 Which GLUTAMIC ACID type do you want for residue 123 0. Not protonated (charge -1) (GLU) 1. Protonated (charge 0) (GLUH) Type a number:0 Which GLUTAMIC ACID type do you want for residue 143 0. Not protonated (charge -1) (GLU) 1. Protonated (charge 0) (GLUH) Type a number:0 Which GLUTAMIC ACID type do you want for residue 161 0. Not protonated (charge -1) (GLU) 1. Protonated (charge 0) (GLUH) Type a number:0 Which GLUTAMIC ACID type do you want for residue 165 0. Not protonated (charge -1) (GLU) 1. Protonated (charge 0) (GLUH) Type a number:0 Which GLUTAMIC ACID type do you want for residue 187 0. Not protonated (charge -1) (GLU) 1. Protonated (charge 0) (GLUH) Type a number:0 Which GLUTAMIC ACID type do you want for residue 195 0. Not protonated (charge -1) (GLU) 1. Protonated (charge 0) (GLUH) Type a number:0 Which GLUTAMIC ACID type do you want for residue 213 0. Not protonated (charge -1) (GLU) 1. Protonated (charge 0) (GLUH) Type a number:0 Which GLUTAMIC ACID type do you want for residue 215 0. Not protonated (charge -1) (GLU) 1. Protonated (charge 0) (GLUH) Type a number:0 Which GLUTAMIC ACID type do you want for residue 220 0. Not protonated (charge -1) (GLU) 1. Protonated (charge 0) (GLUH) Type a number:0 Which GLUTAMIC ACID type do you want for residue 260 0. Not protonated (charge -1) (GLU) 1. Protonated (charge 0) (GLUH) Type a number:0 Which GLUTAMIC ACID type do you want for residue 303 0. Not protonated (charge -1) (GLU) 1. Protonated (charge 0) (GLUH) Type a number:0 Which GLUTAMIC ACID type do you want for residue 366 0. Not protonated (charge -1) (GLU) 1. Protonated (charge 0) (GLUH) Type a number:0 Which GLUTAMIC ACID type do you want for residue 430 0. Not protonated (charge -1) (GLU) 1. Protonated (charge 0) (GLUH) Type a number:0 Which HISTIDINE type do you want for residue 55 0. H on ND1 only (HISD) 1. H on NE2 only (HISE) 2. H on ND1 and NE2 (HISH) 3. Coupled to Heme (HIS1) Type a number:0 Which HISTIDINE type do you want for residue 91 0. H on ND1 only (HISD) 1. H on NE2 only (HISE) 2. H on ND1 and NE2 (HISH) 3. Coupled to Heme (HIS1) Type a number:0 Which HISTIDINE type do you want for residue 189 0. H on ND1 only (HISD) 1. H on NE2 only (HISE) 2. H on ND1 and NE2 (HISH) 3. Coupled to Heme (HIS1) Type a number:0 Which HISTIDINE type do you want for residue 198 0. H on ND1 only (HISD) 1. H on NE2 only (HISE) 2. H on ND1 and NE2 (HISH) 3. Coupled to Heme (HIS1) Type a number:1 Which HISTIDINE type do you want for residue 382 0. H on ND1 only (HISD) 1. H on NE2 only (HISE) 2. H on ND1 and NE2 (HISH) 3. Coupled to Heme (HIS1) Type a number:1 Which HISTIDINE type do you want for residue 418 0. H on ND1 only (HISD) 1. H on NE2 only (HISE) 2. H on ND1 and NE2 (HISH) 3. Coupled to Heme (HIS1) Type a number:1 Which HISTIDINE type do you want for residue 438 0. H on ND1 only (HISD) 1. H on NE2 only (HISE) 2. H on ND1 and NE2 (HISH) 3. Coupled to Heme (HIS1) Type a number:0 ------------------------------------------------------- Program: gmx pdb2gmx, version 2021 Source file: src/gromacs/gmxpreprocess/pdb2gmx.cpp (line 951) Fatal error: The residues in the chain ASP1--CYS214 do not have a consistent type. The first residue has type 'Protein', while residue LYSN45 is of type 'Other'. Either there is a mistake in your chain, or it includes nonstandard residue names that have not yet been added to the residuetypes.dat file in the GROMACS library directory. If there are other molecules such as ligands, they should not have the same chain ID as the adjacent protein chain since it's a separate molecule. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors -------------------------------------------------------