:-) G R O M A C S (-: Good gRace! Old Maple Actually Chews Slate :-) VERSION 3.3.3 (-: Written by David van der Spoel, Erik Lindahl, Berk Hess, and others. Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2008, The GROMACS development team, 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. :-) editconf (-: Option Filename Type Description ------------------------------------------------------------ -f cpeptide.gro Input Generic structure: gro g96 pdb tpr tpb tpa xml -n index.ndx Input, Opt. Index file -o cpeptide.gro Output, Opt! Generic structure: gro g96 pdb xml -mead mead.pqr Output, Opt. Coordinate file for MEAD -bf bfact.dat Input, Opt. Generic data file Option Type Value Description ------------------------------------------------------ -[no]h bool no Print help info and quit -[no]X bool no Use dialog box GUI to edit command line options -nice int 0 Set the nicelevel -[no]w bool no View output xvg, xpm, eps and pdb files -[no]ndef bool no Choose output from default index groups -bt enum triclinic Box type for -box and -d: triclinic, cubic, dodecahedron or octahedron -box vector 0 0 0 Box vector lengths (a,b,c) -angles vector 90 90 90 Angles between the box vectors (bc,ac,ab) -d real 0.5 Distance between the solute and the box -[no]c bool no Center molecule in box (implied by -box and -d) -center vector 0 0 0 Coordinates of geometrical center -translate vector 0 0 0 Translation -rotate vector 0 0 0 Rotation around the X, Y and Z axes in degrees -[no]princ bool no Orient molecule(s) along their principal axes -scale vector 1 1 1 Scaling factor -density real 1000 Density (g/l) of the output box achieved by scaling -[no]vol bool yes Compute and print volume of the box -[no]pbc bool no Remove the periodicity (make molecule whole again) -[no]grasp bool no Store the charge of the atom in the B-factor field and the radius of the atom in the occupancy field -rvdw real 0.12 Default Van der Waals radius (in nm) if one can not be found in the database or if no parameters are present in the topology file -sig56 real 0 Use rmin/2 (minimum in the Van der Waals potential) rather than sigma/2 -[no]vdwread bool no Read the Van der Waals radii from the file vdwradii.dat rather than computing the radii based on the force field -[no]atom bool no Force B-factor attachment per atom -[no]legend bool no Make B-factor legend -label string A Add chain label for all residues Opening library file /usr/local/packages/gromacs/share/gromacs/top/aminoacids.dat Opening library file /usr/local/packages/gromacs/share/gromacs/top/atommass.dat Opening library file /usr/local/packages/gromacs/share/gromacs/top/vdwradii.dat Opening library file /usr/local/packages/gromacs/share/gromacs/top/dgsolv.dat Back Off! I just backed up cpeptide.gro to ./#cpeptide.gro.1# gcq#2: "Jesus Built My Hotrod" (Ministry) WARNING: masses will be determined based on residue and atom names, this can deviate from the real mass of the atom type #Entries in atommass.dat: 83 vdwradii.dat: 28 dgsolv.dat: 7 Read 143 atoms Volume: 3.79506 nm^3, corresponds to roughly 1700 electrons No velocities found system size : 1.429 2.163 1.228 (nm) center : 2.469 1.077 2.517 (nm) box vectors : 1.429 2.164 1.227 (nm) box angles : 90.00 90.00 90.00 (degrees) box volume : 3.80 (nm^3) shift : -1.254 0.504 -1.403 (nm) new center : 1.214 1.582 1.114 (nm) new box vectors : 2.429 3.163 2.228 (nm) new box angles : 90.00 90.00 90.00 (degrees) new box volume : 17.12 (nm^3) WARNING: No boxtype specified - distance condition applied in each dimension. If the molecule rotates the actual distance will be smaller. You might want to use a cubic box instead, or why not try a dodecahedron today? :-) G R O M A C S (-: Gnomes, ROck Monsters And Chili Sauce :-) VERSION 3.3.3 (-: Written by David van der Spoel, Erik Lindahl, Berk Hess, and others. Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2008, The GROMACS development team, 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. :-) genbox (-: Option Filename Type Description ------------------------------------------------------------ -cp cpeptide.gro Input, Opt! Generic structure: gro g96 pdb tpr tpb tpa xml -cs spc216.gro Input, Opt!, Lib. Generic structure: gro g96 pdb tpr tpb tpa xml -ci insert.gro Input, Opt. Generic structure: gro g96 pdb tpr tpb tpa xml -o cpeptide_b4em.gro Output Generic structure: gro g96 pdb xml -p cpeptide.top In/Out, Opt! Topology file Option Type Value Description ------------------------------------------------------ -[no]h bool no Print help info and quit -[no]X bool no Use dialog box GUI to edit command line options -nice int 19 Set the nicelevel -box vector 0 0 0 box size -nmol int 0 no of extra molecules to insert -try int 10 try inserting -nmol*-try times -seed int 1997 random generator seed -vdwd real 0.105 default vdwaals distance -shell real 0 thickness of optional water layer around solute -maxsol int 0 maximum number of solvent molecules to add if they fit in the box. If zero (default) this is ignored -[no]vel bool no keep velocities from input solute and solvent Opening library file /usr/local/packages/gromacs/share/gromacs/top/aminoacids.dat Opening library file /usr/local/packages/gromacs/share/gromacs/top/atommass.dat Opening library file /usr/local/packages/gromacs/share/gromacs/top/vdwradii.dat Opening library file /usr/local/packages/gromacs/share/gromacs/top/dgsolv.dat Reading solute configuration Gallium Rubidium Oxygen Manganese Argon Carbon Silicon Containing 143 atoms in 13 residues Initialising van der waals distances... Reading solvent configuration "216H2O,WATJP01,SPC216,SPC-MODEL,300K,BOX(M)=1.86206NM,WFVG,MAR. 1984" solvent configuration contains 648 atoms in 216 residues Initialising van der waals distances... Will generate new solvent configuration of 2x2x2 boxes Generating configuration Sorting configuration Found 1 molecule type: SOL ( 3 atoms): 1728 residues Calculating Overlap... box_margin = 0.315 Removed 2895 atoms that were outside the box Succesfully made neighbourlist nri = 11445, nrj = 456434 Checking Protein-Solvent overlap: tested 4083 pairs, removed 231 atoms. Checking Solvent-Solvent overlap: tested 36790 pairs, removed 597 atoms. Added 487 molecules Generated solvent containing 1461 atoms in 487 residues Writing generated configuration to cpeptide_b4em.gro Gallium Rubidium Oxygen Manganese Argon Carbon Silicon Output configuration contains 1604 atoms in 500 residues Volume : 17.1176 (nm^3) Density : 1002.52 (g/l) Number of SOL molecules: 487 Processing topology Back Off! I just backed up cpeptide.top to ./#cpeptide.top.1# gcq#144: "I Wrapped a Newspaper Round My Head" (F. Zappa) WARNING: masses will be determined based on residue and atom names, this can deviate from the real mass of the atom type #Entries in atommass.dat: 83 vdwradii.dat: 28 dgsolv.dat: 7 Neighborsearching with a cut-off of 0.48 Table routines are used for coulomb: FALSE Table routines are used for vdw: FALSE Cut-off's: NS: 0.48 Coulomb: 0.48 LJ: 0.48 System total charge: 0.000 Grid: 10 x 13 x 9 cells Adding line for 487 solvent molecules to topology file (cpeptide.top)