jonathan@jonathan-desktop:~/Documents/gromacs_files/biotin_avidin_md$ grompp -f em.mdp -c system.gro -p system.top -o em.tpr -maxwarn 2 :-) G R O M A C S (-: Good gRace! Old Maple Actually Chews Slate :-) 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 (-: Option Filename Type Description ------------------------------------------------------------ -f em.mdp Input grompp input file with MD parameters -po mdout.mdp Output grompp input file with MD parameters -c system.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 system.top Input Topology file -pp processed.top Output, Opt. Topology file -o em.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 2 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 Generated 2926 of the 2926 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 2926 of the 2926 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'Protein_chain_A' Excluding 3 bonded neighbours molecule type 'Protein_chain_B' Excluding 3 bonded neighbours molecule type 'Protein_chain_C' Excluding 3 bonded neighbours molecule type 'Protein_chain_D' Excluding 2 bonded neighbours molecule type 'SOL' Excluding 3 bonded neighbours molecule type 'biotin' NOTE 1 [file system.top, line 54]: System has non-zero total charge: -4.000021 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. Warning: atom name 6960 in system.top and system.gro does not match (OW - C) Warning: atom name 6961 in system.top and system.gro does not match (HW1 - O) Warning: atom name 6962 in system.top and system.gro does not match (HW2 - N) Warning: atom name 6963 in system.top and system.gro does not match (OW - H) Warning: atom name 6964 in system.top and system.gro does not match (HW1 - N1) Warning: atom name 6965 in system.top and system.gro does not match (HW2 - H1) Warning: atom name 6966 in system.top and system.gro does not match (OW - C1) Warning: atom name 6967 in system.top and system.gro does not match (HW1 - H2) Warning: atom name 6968 in system.top and system.gro does not match (HW2 - C2) Warning: atom name 6969 in system.top and system.gro does not match (OW - H3) Warning: atom name 6970 in system.top and system.gro does not match (HW1 - C3) Warning: atom name 6971 in system.top and system.gro does not match (HW2 - H4) Warning: atom name 6972 in system.top and system.gro does not match (OW - H5) Warning: atom name 6973 in system.top and system.gro does not match (HW1 - C4) Warning: atom name 6974 in system.top and system.gro does not match (HW2 - H6) Warning: atom name 6975 in system.top and system.gro does not match (OW - S) Warning: atom name 6976 in system.top and system.gro does not match (HW1 - C5) Warning: atom name 6977 in system.top and system.gro does not match (HW2 - H7) Warning: atom name 6978 in system.top and system.gro does not match (OW - H8) Warning: atom name 6979 in system.top and system.gro does not match (HW1 - C6) (more than 20 non-matching atom names) WARNING 1 [file system.top, line 54]: 47024 non-matching atom names atom names from system.top will be used atom names from system.gro will be ignored Analysing residue names: There are: 480 Protein residues There are: 15568 Water residues There are: 10 Other residues Analysing Protein... Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... Number of degrees of freedom in T-Coupling group rest is 161946.00 Largest charge group radii for Van der Waals: 5.520, 3.810 nm Largest charge group radii for Coulomb: 7.576, 7.576 nm WARNING 2 [file em.mdp]: The sum of the two largest charge group radii (15.152546) is larger than rlist (1.000000) Calculating fourier grid dimensions for X Y Z Using a fourier grid of 80x80x80, spacing 0.111 0.111 0.111 Estimate for the relative computational load of the PME mesh part: 0.26 NOTE 2 [file em.mdp]: This run will generate roughly 3125 Mb of data There were 2 notes There were 2 warnings gcq#116: "If You're So Special Why aren't You Dead ?" (The Breeders)