Option Filename Type Description ------------------------------------------------------------ -f 01em.mdp Input grompp input file with MD parameters -po mdout.mdp Output grompp input file with MD parameters -c conf.gro Input Structure file: gro g96 pdb tpr etc. -r conf.gro Input, Opt. Structure file: gro g96 pdb tpr etc. -rb conf.gro Input, Opt. Structure file: gro g96 pdb tpr etc. -n index.ndx Input, Opt. Index file -p topol.top Input Topology file -pp processed.top Output, Opt. Topology file -o topol.tpr Output Run input file: tpr tpb tpa -t traj.trr Input, Opt. Full precision trajectory: trr trj cpt -e ener.edr Input, Opt. Energy file Option Type Value Description ------------------------------------------------------ -[no]h bool no Print help info and quit -[no]version bool no Print version info and quit -nice int 0 Set the nicelevel -[no]v bool no Be loud and noisy -time real -1 Take frame at or first after this time. -[no]rmvsbds bool yes Remove constant bonded interactions with virtual sites -maxwarn int 0 Number of allowed warnings during input processing. Not for normal use and may generate unstable systems -[no]zero bool no Set parameters for bonded interactions without defaults to zero instead of generating an error -[no]renum bool yes Renumber atomtypes and minimize number of atomtypes Back Off! I just backed up mdout.mdp to ./#mdout.mdp.2# Generated 34453 of the 34453 non-bonded parameter combinations Generating 1-4 interactions: fudge = 1 Generated 31280 of the 34453 1-4 parameter combinations ERROR 1 [file topol.top, line 252]: No default Angle types ERROR 2 [file topol.top, line 258]: No default Angle types ERROR 3 [file topol.top, line 259]: No default Angle types ERROR 4 [file topol.top, line 262]: No default Angle types ERROR 5 [file topol.top, line 264]: No default Angle types ERROR 6 [file topol.top, line 266]: No default Angle types ERROR 7 [file topol.top, line 268]: No default Angle types ERROR 8 [file topol.top, line 271]: No default Angle types ERROR 9 [file topol.top, line 273]: No default Angle types ERROR 10 [file topol.top, line 275]: No default Angle types ERROR 11 [file topol.top, line 278]: No default Angle types ERROR 12 [file topol.top, line 279]: No default Angle types ERROR 13 [file topol.top, line 281]: No default Angle types ERROR 14 [file topol.top, line 284]: No default Angle types ERROR 15 [file topol.top, line 285]: No default Angle types ERROR 16 [file topol.top, line 287]: No default Angle types ERROR 17 [file topol.top, line 292]: No default Angle types ERROR 18 [file topol.top, line 295]: No default Angle types ERROR 19 [file topol.top, line 296]: No default Angle types ERROR 20 [file topol.top, line 299]: No default Angle types ERROR 21 [file topol.top, line 301]: No default Angle types ERROR 22 [file topol.top, line 303]: No default Angle types ERROR 23 [file topol.top, line 305]: No default Angle types ERROR 24 [file topol.top, line 308]: No default Angle types ERROR 25 [file topol.top, line 310]: No default Angle types ERROR 26 [file topol.top, line 312]: No default Angle types ERROR 27 [file topol.top, line 315]: No default Angle types ERROR 28 [file topol.top, line 316]: No default Angle types ERROR 29 [file topol.top, line 318]: No default Angle types ERROR 30 [file topol.top, line 322]: No default Angle types ERROR 31 [file topol.top, line 323]: No default Angle types ERROR 32 [file topol.top, line 325]: No default Angle types ERROR 33 [file topol.top, line 332]: No default Proper Dih. types ERROR 34 [file topol.top, line 333]: No default Proper Dih. types ERROR 35 [file topol.top, line 334]: No default Proper Dih. types ERROR 36 [file topol.top, line 335]: No default Proper Dih. types ERROR 37 [file topol.top, line 336]: No default Proper Dih. types ERROR 38 [file topol.top, line 337]: No default Proper Dih. types ERROR 39 [file topol.top, line 338]: No default Proper Dih. types ERROR 40 [file topol.top, line 339]: No default Proper Dih. types ERROR 41 [file topol.top, line 340]: No default Proper Dih. types ERROR 42 [file topol.top, line 341]: No default Proper Dih. types ERROR 43 [file topol.top, line 342]: No default Proper Dih. types ERROR 44 [file topol.top, line 343]: No default Proper Dih. types ERROR 45 [file topol.top, line 344]: No default Proper Dih. types ERROR 46 [file topol.top, line 345]: No default Proper Dih. types ERROR 47 [file topol.top, line 346]: No default Proper Dih. types ERROR 48 [file topol.top, line 347]: No default Proper Dih. types ERROR 49 [file topol.top, line 348]: No default Proper Dih. types ERROR 50 [file topol.top, line 349]: No default Proper Dih. types ERROR 51 [file topol.top, line 350]: No default Proper Dih. types ERROR 52 [file topol.top, line 351]: No default Proper Dih. types ERROR 53 [file topol.top, line 352]: No default Proper Dih. types ERROR 54 [file topol.top, line 353]: No default Proper Dih. types ERROR 55 [file topol.top, line 354]: No default Proper Dih. types ERROR 56 [file topol.top, line 355]: No default Proper Dih. types ERROR 57 [file topol.top, line 356]: No default Proper Dih. types ERROR 58 [file topol.top, line 357]: No default Proper Dih. types ERROR 59 [file topol.top, line 358]: No default Proper Dih. types ERROR 60 [file topol.top, line 359]: No default Proper Dih. types ERROR 61 [file topol.top, line 360]: No default Proper Dih. types ERROR 62 [file topol.top, line 361]: No default Proper Dih. types ERROR 63 [file topol.top, line 362]: No default Proper Dih. types ERROR 64 [file topol.top, line 363]: No default Proper Dih. types ERROR 65 [file topol.top, line 364]: No default Proper Dih. types ERROR 66 [file topol.top, line 365]: No default Proper Dih. types ERROR 67 [file topol.top, line 366]: No default Proper Dih. types ERROR 68 [file topol.top, line 367]: No default Proper Dih. types ERROR 69 [file topol.top, line 368]: No default Proper Dih. types ERROR 70 [file topol.top, line 369]: No default Proper Dih. types ERROR 71 [file topol.top, line 370]: No default Proper Dih. types ERROR 72 [file topol.top, line 371]: No default Proper Dih. types ERROR 73 [file topol.top, line 372]: No default Proper Dih. types ERROR 74 [file topol.top, line 373]: No default Proper Dih. types ERROR 75 [file topol.top, line 374]: No default Proper Dih. types ERROR 76 [file topol.top, line 375]: No default Proper Dih. types ERROR 77 [file topol.top, line 376]: No default Proper Dih. types ERROR 78 [file topol.top, line 377]: No default Proper Dih. types ERROR 79 [file topol.top, line 378]: No default Proper Dih. types ERROR 80 [file topol.top, line 379]: No default Proper Dih. types ERROR 81 [file topol.top, line 380]: No default Proper Dih. types ERROR 82 [file topol.top, line 381]: No default Proper Dih. types ERROR 83 [file topol.top, line 382]: No default Proper Dih. types ERROR 84 [file topol.top, line 383]: No default Proper Dih. types ERROR 85 [file topol.top, line 384]: No default Proper Dih. types ERROR 86 [file topol.top, line 385]: No default Proper Dih. types ERROR 87 [file topol.top, line 386]: No default Proper Dih. types ERROR 88 [file topol.top, line 387]: No default Proper Dih. types ERROR 89 [file topol.top, line 388]: No default Proper Dih. types ERROR 90 [file topol.top, line 389]: No default Proper Dih. types ERROR 91 [file topol.top, line 390]: No default Proper Dih. types ERROR 92 [file topol.top, line 391]: No default Proper Dih. types ERROR 93 [file topol.top, line 392]: No default Proper Dih. types ERROR 94 [file topol.top, line 393]: No default Proper Dih. types ERROR 95 [file topol.top, line 394]: No default Proper Dih. types ERROR 96 [file topol.top, line 395]: No default Proper Dih. types ERROR 97 [file topol.top, line 396]: No default Proper Dih. types ERROR 98 [file topol.top, line 397]: No default Proper Dih. types ERROR 99 [file topol.top, line 398]: No default Proper Dih. types ERROR 100 [file topol.top, line 399]: No default Proper Dih. types ERROR 101 [file topol.top, line 400]: No default Proper Dih. types ERROR 102 [file topol.top, line 401]: No default Proper Dih. types ERROR 103 [file topol.top, line 402]: No default Proper Dih. types ERROR 104 [file topol.top, line 403]: No default Proper Dih. types ERROR 105 [file topol.top, line 404]: No default Proper Dih. types ERROR 106 [file topol.top, line 405]: No default Proper Dih. types ERROR 107 [file topol.top, line 406]: No default Proper Dih. types ERROR 108 [file topol.top, line 407]: No default Proper Dih. types ERROR 109 [file topol.top, line 408]: No default Proper Dih. types ERROR 110 [file topol.top, line 409]: No default Proper Dih. types ERROR 111 [file topol.top, line 410]: No default Proper Dih. types ERROR 112 [file topol.top, line 411]: No default Proper Dih. types ERROR 113 [file topol.top, line 412]: No default Proper Dih. types ERROR 114 [file topol.top, line 413]: No default Proper Dih. types ERROR 115 [file topol.top, line 414]: No default Proper Dih. types ERROR 116 [file topol.top, line 415]: No default Proper Dih. types ERROR 117 [file topol.top, line 416]: No default Proper Dih. types ERROR 118 [file topol.top, line 417]: No default Proper Dih. types ERROR 119 [file topol.top, line 418]: No default Proper Dih. types ERROR 120 [file topol.top, line 419]: No default Proper Dih. types ERROR 121 [file topol.top, line 420]: No default Proper Dih. types ERROR 122 [file topol.top, line 421]: No default Proper Dih. types ERROR 123 [file topol.top, line 422]: No default Proper Dih. types ERROR 124 [file topol.top, line 423]: No default Proper Dih. types ERROR 125 [file topol.top, line 424]: No default Proper Dih. types ERROR 126 [file topol.top, line 425]: No default Proper Dih. types ERROR 127 [file topol.top, line 426]: No default Proper Dih. types ERROR 128 [file topol.top, line 427]: No default Proper Dih. types ERROR 129 [file topol.top, line 428]: No default Proper Dih. types ERROR 130 [file topol.top, line 429]: No default Proper Dih. types ERROR 131 [file topol.top, line 430]: No default Proper Dih. types ERROR 132 [file topol.top, line 431]: No default Proper Dih. types ERROR 133 [file topol.top, line 432]: No default Proper Dih. types ERROR 134 [file topol.top, line 433]: No default Proper Dih. types ERROR 135 [file topol.top, line 434]: No default Proper Dih. types ERROR 136 [file topol.top, line 435]: No default Proper Dih. types ERROR 137 [file topol.top, line 436]: No default Proper Dih. types ERROR 138 [file topol.top, line 437]: No default Proper Dih. types ERROR 139 [file topol.top, line 438]: No default Proper Dih. types ERROR 140 [file topol.top, line 439]: No default Proper Dih. types ERROR 141 [file topol.top, line 440]: No default Proper Dih. types ERROR 142 [file topol.top, line 441]: No default Proper Dih. types ERROR 143 [file topol.top, line 442]: No default Proper Dih. types ERROR 144 [file topol.top, line 443]: No default Proper Dih. types ERROR 145 [file topol.top, line 444]: No default Proper Dih. types ERROR 146 [file topol.top, line 445]: No default Proper Dih. types ERROR 147 [file topol.top, line 446]: No default Proper Dih. types ERROR 148 [file topol.top, line 447]: No default Proper Dih. types ERROR 149 [file topol.top, line 448]: No default Proper Dih. types ERROR 150 [file topol.top, line 449]: No default Proper Dih. types ERROR 151 [file topol.top, line 450]: No default Proper Dih. types ERROR 152 [file topol.top, line 451]: No default Proper Dih. types ERROR 153 [file topol.top, line 452]: No default Proper Dih. types ERROR 154 [file topol.top, line 453]: No default Proper Dih. types ERROR 155 [file topol.top, line 457]: No default Improper Dih. types ERROR 156 [file topol.top, line 458]: No default Improper Dih. types ERROR 157 [file topol.top, line 459]: No default Improper Dih. types ERROR 158 [file topol.top, line 460]: No default Improper Dih. types ERROR 159 [file topol.top, line 461]: No default Improper Dih. types ERROR 160 [file topol.top, line 462]: No default Improper Dih. types ERROR 161 [file topol.top, line 463]: No default Improper Dih. types ERROR 162 [file topol.top, line 464]: No default Improper Dih. types ERROR 163 [file topol.top, line 465]: No default Improper Dih. types ERROR 164 [file topol.top, line 466]: No default Improper Dih. types ERROR 165 [file topol.top, line 467]: No default Improper Dih. types ERROR 166 [file topol.top, line 468]: No default Improper Dih. types ERROR 167 [file topol.top, line 469]: No default Improper Dih. types ERROR 168 [file topol.top, line 470]: No default Improper Dih. types ERROR 169 [file topol.top, line 471]: No default Improper Dih. types ERROR 170 [file topol.top, line 472]: No default Improper Dih. types ERROR 171 [file topol.top, line 473]: No default Improper Dih. types ERROR 172 [file topol.top, line 474]: No default Improper Dih. types ERROR 173 [file topol.top, line 475]: No default Improper Dih. types ERROR 174 [file topol.top, line 476]: No default Improper Dih. types ERROR 175 [file topol.top, line 477]: No default Improper Dih. types ERROR 176 [file topol.top, line 478]: No default Improper Dih. types ERROR 177 [file topol.top, line 479]: No default Improper Dih. types ERROR 178 [file topol.top, line 480]: No default Improper Dih. types ERROR 179 [file topol.top, line 481]: No default Improper Dih. types ERROR 180 [file topol.top, line 482]: No default Improper Dih. types ERROR 181 [file topol.top, line 483]: No default Improper Dih. types ERROR 182 [file topol.top, line 484]: No default Improper Dih. types ERROR 183 [file topol.top, line 485]: No default Improper Dih. types ERROR 184 [file topol.top, line 486]: No default Improper Dih. types ERROR 185 [file topol.top, line 487]: No default Improper Dih. types ERROR 186 [file topol.top, line 488]: No default Improper Dih. types ERROR 187 [file topol.top, line 489]: No default Improper Dih. types ERROR 188 [file topol.top, line 490]: No default Improper Dih. types Excluding 3 bonded neighbours molecule type 'Other' NOTE 1 [file topol.top, line 503]: System has non-zero total charge: -0.190000 Total charge should normally be an integer. See http://www.gromacs.org/Documentation/Floating_Point_Arithmetic for discussion on how close it should be to an integer. ERROR 189 [file topol.top, line 503]: ERROR: The cut-off length is longer than half the shortest box vector or longer than the smallest box diagonal element. Increase the box size or decrease rlist. There was 1 note ------------------------------------------------------- Program grompp, VERSION 4.5.5 Source code file: grompp.c, line: 1372 Fatal error: There were 189 errors in input file(s) For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors ------------------------------------------------------- "Everything Must Go" (Red Hot Chili Peppers) :-) G R O M A C S (-: GROningen Mixture of Alchemy and Childrens' Stories :-) VERSION 4.5.5 (-: Written by Emile Apol, Rossen Apostolov, Herman J.C. Berendsen, Aldert van Buuren, Pär Bjelkmar, Rudi van Drunen, Anton Feenstra, Gerrit Groenhof, Peter Kasson, Per Larsson, Pieter Meulenhoff, Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz, Michael Shirts, Alfons Sijbers, Peter Tieleman, Berk Hess, David van der Spoel, and Erik Lindahl. Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2010, The GROMACS development team at Uppsala University & The Royal Institute of Technology, Sweden. check out http://www.gromacs.org for more information. This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version. :-) grompp (-: