Hi users, To answer Mark's question about reading section 3.2. Yes I have.I wish to conduct an SMD study.I want to place my protein system at one end of the longest side of triclinic shell and then pull parallel to the longest side.
Yang I have used both pymol and VMD for visualization Tsjerk when i dont use the -d option the box is created with the protein completely outside the box and at a distance. I was therefore thinking of either the -d option or -c option. I dont want to center my protein in the box but keep it as far as possible (allowing buffer) on one side of the rectangle so that I can pull through the solvent using SMD..for the editconf i get a message that the box type was not defined although i have given -bt triclinic. see below [EMAIL PROTECTED]:~/bcl2/solvation> editconf -f two.pdb -o three.pdb -d 0.9 -box 20 10 10 -bt triclinic :-) G R O M A C S (-: Getting the Right Output Means no Artefacts in Calculating Stuff :-) VERSION 3.3.1 (-: Written by David van der Spoel, Erik Lindahl, Berk Hess, and others. Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2006, 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 two.pdb Input Generic structure: gro g96 pdb tpr tpb tpa xml -n index.ndx Input, Opt. Index file -o three.pdb 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 -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 20 10 10 Box vector lengths (a,b,c) -angles vector 90 90 90 Angles between the box vectors (bc,ac,ab) -d real 0.9 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 WARNING: masses will be determined based on residue and atom names, this can deviate from the real mass of the atom type In case you use free energy of solvation predictions: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ D. Eisenberg and A. D. McLachlan Solvation energy in protein folding and binding Nature 319 (1986) pp. 199-203 -------- -------- --- Thank You --- -------- -------- Opening library file /usr/local/appl/gromacs-3.3.1/share/gromacs/top/aminoacids.dat Opening library file /usr/local/appl/gromacs-3.3.1/share/gromacs/top/atommass.dat Opening library file /usr/local/appl/gromacs-3.3.1/share/gromacs/top/vdwradii.dat Opening library file /usr/local/appl/gromacs-3.3.1/share/gromacs/top/dgsolv.dat #Entries in atommass.dat: 82 vdwradii.dat: 26 dgsolv.dat: 7 Read 1307 atoms Volume: 0.001 nm^3, corresponds to roughly 0 electrons No velocities found system size : 4.956 4.351 4.507 (nm) center : -0.412 -0.852 -0.082 (nm) box vectors : 0.100 0.100 0.100 (nm) box angles : 90.00 90.00 90.00 (degrees) box volume : 0.00 (nm^3) shift : 3.790 3.928 3.236 (nm) new center : 3.378 3.075 3.154 (nm) new box vectors : 6.756 6.151 6.307 (nm) new box angles : 90.00 90.00 90.00 (degrees) new box volume : 262.11 (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? Back Off! I just backed up three.pdb to ./#three.pdb.1# gcq#289: "Do You Have a Mind of Your Own ?" (Garbage) Prasenjit Kumar Mukherjee Graduate Student Department of Medicinal Chemistry School of Pharmacy University of Mississippi USA Cell - 662 380 0146 Office - 662 915 1286 _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php