[gmx-users] insert silicon atoms into ice structure

[Santan William]

Dear GMXusers,
        I wanna insert several silicon atoms into an ice crystal. I use
genbox with a Silicon.pdb, but there's no any silicon atom in the out file.
Do I miss anything? Anyone has some comments? Thanks a lot.

Best,
william


        Here's output log:

root at xwei:~/Desktop/gromacs/icesi# genbox -cp ice.pdb -ci Si.pdb -o
icesi.pdb -nmol 10

Option     Filename  Type         Description
------------------------------------------------------------
 -cp        ice.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         Si.pdb  Input, Opt!  Generic structure: gro g96 pdb tpr tpb tpa
                                   xml
  -o      icesi.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
      -[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     10  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/share/gromacs/top/aminoacids.dat
Opening library file /usr/share/gromacs/top/atommass.dat
Opening library file /usr/share/gromacs/top/vdwradii.dat
Opening library file /usr/share/gromacs/top/dgsolv.dat
#Entries in atommass.dat: 82 vdwradii.dat: 26 dgsolv.dat: 7
Reading solute configuration
Gromacs Runs On Most of All Computer Systems
Containing 1080 atoms in 360 residues
Initialising van der waals distances...
Reading molecule configuration

Containing 40 atoms in 1 residue
Initialising van der waals distances...
Try 15box_margin = 0.48
Removed 0 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: 9 x 9 x 9 cells
nri = 2105, nrj = 25364
Checking Protein-Solvent overlap: tested 20 pairs, removed 40 atoms.
Checking Solvent-Solvent overlap: tested 0 pairs, removed 0 atoms.
Try 99
Added 0 molecules (out of 10 requested) of
Writing generated configuration to icesi.pdb
Gromacs Runs On Most of All Computer Systems

Output configuration contains 1080 atoms in 360 residues
Volume                 :     11.4017 (nm^3)
Density                :     944.556 (g/l)
Number of SOL molecules:    360
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