[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  (-:

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      Written by David van der Spoel, Erik Lindahl, Berk
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                               :-)  editconf  (-:

Option     Filename  Type         Description
  -f        two.pdb  Input        Generic structure: gro g96
pdb tpr tpb tpa
  -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
         -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
          -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
  -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
    -[no]vol   bool    yes  Compute and print volume of the
    -[no]pbc   bool     no  Remove the periodicity (make
molecule whole
  -[no]grasp   bool     no  Store the charge of the atom in
the B-factor
                            field and the radius of the atom
in the occupancy
       -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
 -[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
         this can deviate from the real mass of the atom
In case you use free energy of solvation predictions:

D. Eisenberg and A. D. McLachlan
Solvation energy in protein folding and binding
Nature 319 (1986) pp. 199-203
-------- -------- --- Thank You --- -------- --------

Opening library file
Opening library file
Opening library file
Opening library file
#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

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

Cell   - 662 380 0146
Office - 662 915 1286 

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