[gmx-users] Solvent_box
pkmukher
pkmukher at olemiss.edu
Thu Jul 12 17:03:55 CEST 2007
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
r1028 at redwood:~/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
More information about the gromacs.org_gmx-users
mailing list