[Xplor-nih] Water

[Usman Rasul]

Hi..

I am trying to generate a box of water molecules. I have used a script  
someone made and also has the same problem.

The script is written as:-


topology  @toph19.sol

  end

  parameters

  @param19.sol

  end


    nbonds                                  {*This statement specifies the  *}
       atom cdie shift eps=1.0  e14fac=0.4  {*nonbonded interaction energy  *}
       cutnb=7.5 ctonnb=6.0 ctofnb=6.5      {*options.  Note the reduced    *}
       nbxmod=5 vswitch                     {*nonbonding cutoff to save some*}
    end                                     {*CPU time.   This statement    *}
                                            {*overwrites the defaults in    *}
                                            {*the parameter file.           *}

  end

  segment

       name="WAT"
       chain  end
         molecule name = TIP3  number=30 end
  end

  xrefine
    {* define unit cell dimensions *}
    a=14.0 b=16.0 c=20.0 alpha=80.0 beta=95.0 gamma=110.0
    {* define space group "P1" *}
   symmetry=(x,y,z)
  end

  {* a structure with randomly distributed coordinates *}
   coor fractional end
   vector do (x=random()) ( all )              {* Generate fake coordinates *}
   vector do (y=random()) ( all )              {* to avoid error messages   *}
   vector do (z=random()) ( all )              {* about unknown atoms.      *}
   coord orthogonal
  end

  write structure output= water.psf  end

  write coordinates output= water.pdb end


I get a .pdb file with the oxygen atoms and hydrogen atoms completely  
separated. I thought the topology file allows for bonds between two  
hydrogens and oxygen atom..

I'm a beginner with writing scripts so would really appreciate the help.

Usman Rasul