[gmx-users] insert silicon atoms into ice structure

[Justin A. Lemkul]

Santan William wrote:
> 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.
> 

If zero atoms were inserted, there probably isn't enough space for them in the box.

-Justin

> 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
> 

-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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