[gmx-users] Fwd: GROMACS_solvent_box

Tsjerk Wassenaar tsjerkw at gmail.com
Thu Jul 12 19:45:35 CEST 2007


Hi Prasenjit,

What do you expect? You don't give any clue to what you think goes
wrong or, in other words, is not according to your expectations. As
far as I can see from the output, you get what you request. A
rectangular box with edge lengths of 20, 10 and 10 nm, giving a total
of 2000 nm^3, which is filled with solvent, giving appx 200k atoms in
total. What did you want to have?

Tsjerk

---------- Forwarded message ----------
From: pkmukher <pkmukher at olemiss.edu>
Date: Jul 12, 2007 5:52 PM
Subject: GROMACS_solvent_box
To: tsjerkw at gmail.com


Hello Tsjerk,

  I am writing to you separately since i wanted to send you
a structure file.I tried the -angles option for editconf

editconf -f two.pdb -o three.pdb -translate 10 10 10
editconf -f three.pdb -o four.pdb -bt triclinic -box 20 10
10 -angles 90 90 90 -c
genbox -cp four.pdb -cs spc216.gro -o five.pdb

I have attched the output for the three commands and the
final pdb five.pdb.Could you give me your suggestions as to
what is going wrong here.THanks and regards.Prasenjit

Prasenjit Kumar Mukherjee
Graduate Student
Department of Medicinal Chemistry
School of Pharmacy
University of Mississippi
USA

Cell   - 662 380 0146
Office - 662 915 1286










-- 
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623
-------------- next part --------------
r1028 at redwood:~/bcl2/solvation> editconf -f two.pdb -o three.pdb -translate 10 10 10
                         :-)  G  R  O  M  A  C  S  (-:

                Gravel Rubs Often Many Awfully Cauterized Sores

                            :-)  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  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  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 10 10 10  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
Translating 1307 atoms (out of 1307) by 10 10 10 nm

gcq#283: "Working in the Burger Kings, Spitting on your Onion Rings" (Slim Shady)

r1028 at redwood:~/bcl2/solvation> editconf -f three.pdb -o four.pdb -bt triclinic -box 20 10 10 -angles 90 90 90 -c
                         :-)  G  R  O  M  A  C  S  (-:

                      GROup of MAchos and Cynical Suckers

                            :-)  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      three.pdb  Input        Generic structure: gro g96 pdb tpr tpb tpa
                                   xml
  -n      index.ndx  Input, Opt.  Index file
  -o       four.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  Distance between the solute and the box
      -[no]c   bool    yes  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  4.508 (nm)
    center      :  9.588  9.148  9.918 (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       :  0.412 -4.148 -4.918 (nm)
new center      : 10.000  5.000  5.000 (nm)
new box vectors : 20.000 10.000 10.000 (nm)
new box angles  :  90.00  90.00  90.00 (degrees)
new box volume  :2000.00               (nm^3)

gcq#78: "I Snipe Like Wesley" (Urban Dance Squad)

r1028 at redwood:~/bcl2/solvation> genbox -cp four.pdb -cs spc216.gro -o five.pdb
                         :-)  G  R  O  M  A  C  S  (-:

                   Good gRace! Old Maple Actually Chews Slate

                            :-)  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.

                                :-)  genbox  (-:

Option     Filename  Type         Description
------------------------------------------------------------
 -cp       four.pdb  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       five.pdb  Output       Generic structure: gro g96 pdb xml
  -p      topol.top  In/Out, Opt. Topology file

      Option   Type  Value  Description
------------------------------------------------------
      -[no]h   bool     no  Print help info and quit
       -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

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
Reading solute configuration
GROwing Monsters And Cloning Shrimps
Containing 1307 atoms in 162 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 11x6x6 boxes
Generating configuration
Sorting configuration
Found 1 molecule type:
    SOL (   3 atoms): 85536 residues
Calculating Overlap...
box_margin = 0.315
Removed 42381 atoms that were outside the box
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: 83 x 41 x 41 cells
Succesfully made neighbourlist
nri = 318818, nrj = 8875303
Checking Protein-Solvent overlap: tested 29087 pairs, removed 2658 atoms.
Checking Solvent-Solvent overlap: tested 1283062 pairs, removed 14868 atoms.
Added 65567 molecules
Generated solvent containing 196701 atoms in 65567 residues
Writing generated configuration to five.pdb
GROwing Monsters And Cloning Shrimps

Output configuration contains 198008 atoms in 65729 residues
Volume                 :        2000 (nm^3)
Density                :     996.092 (g/l)
Number of SOL molecules:  65567   


gcq#148: "We Have No Money" (E. Clementi)


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